M A Y 2 0 0 1

Can you believe his eyes

or his nose

or his smile?

Facing the Truth Using Science to Evaluate Expressions

Hypertension • DNA’s Machinery • Classroom Design • Molecular Art 18 Touching the Invisible One Molecule at a Time

Carlos Bustamante, who took apart toy cars as a boy, is now exploring the machinery of DNA. Cover: Courtesy of Paul Ekman M AY 2 0 0 1 FEATURES VOLUME 14 NUMBER 2

12 Facing the Truth 22 Solving 28 Overcoming the A New Tool to Analyze Hypertension’s Intractable Our Expressions Deadly Puzzle Problem Rick Lifton’s Team at Increasing the Numbers of Yale Is Putting the Pieces Underrepresented Minorities Together in Science 34 N OTA B ENE

2 Awards and Honors 39 Teens Tend to Be Night Owls HHMI TRUSTEES ETTERFROM James A. Baker, III, Esq. L HHMI Awards $15 Million to Senior Partner THE P RESIDENT Baker & Botts European Researchers Alexander G. Bearn, M.D. Executive Officer American Philosophical Society 3 The Other Genome Race Adjunct Professor 40 Untangling the Web of Yeast The Rockefeller University Professor Emeritus of Medicine Protein Interactions Cornell University Medical College Frank William Gay Former President and Chief Executive Officer U P F RONT SUMMA Corporation 41 Vaccination Experiment Casts James H. Gilliam, Jr., Esq. Former Executive Vice President 4 The Human Genome Goes to a Key Guilty Vote Against and General Counsel, Beneficial Corporation Hanna H. Gray, Ph.D., Chairman Amyloid in Alzheimer’s President Emeritus and High School Harry Pratt Judson Distinguished Service Professor of History The University of Chicago 6 Fruit Fly Gene Survey Finds Garnett L. Keith Bringing Biology’s Models to Chairman Correlation Between Aging SeaBridge Investment Advisors, L.L.C. Wall Street and Beyond Former Vice Chairman and and Free Radicals Chief Investment Officer The Prudential Insurance Company of America 8 Jeremy R. Knowles, D.Phil. Shane Crotty Has a Hot Paper Dean of the Faculty of Arts and Sciences and a New Biography, Too and Amory Houghton Professor of C LOSE -U P Chemistry and Biochemistry Harvard University William R. Lummis, Esq. Former Chairman of the Board of Directors 42 The Art of Science and Chief Executive Officer P ERSPECTIVE The Howard Hughes Corporation Irving S. Shapiro, Esq., Chairman Emeritus Of Counsel Skadden, Arps, Slate, Meagher & Flom 10 Genetically Modified Crops Former Chairman and Chief Executive Officer O BJECT L ESSON E.I. du Pont de Nemours and Company Anne M. Tatlock Chairman and Chief Executive Officer F ROMTHE T OOLBOX 46 Redesigning Laboratory Fiduciary Trust Company International Classrooms HHMI OFFICERS Thomas R. Cech, Ph.D., President 34 Peter J. Bruns, Ph.D., Vice President for Grants Dam! A New Method and Special Programs for Pinpointing David A. Clayton, Ph.D., Vice President for Science Development I NSIDE HHMI Stephen M. Cohen, Vice President and Chief Financial Officer Gene Transcription Joan S. Leonard, Esq., Vice President and General Counsel Gerald M. Rubin, Ph.D., Vice President for Biomedical Research 48 Peter Bruns Seeks to Bind Nestor V. Santiago, Vice President and Chief Investment Officer N EWS & N OTES Science to Education HHMI BULLETIN STAFF David Jarmul, issue editor Kimberly Blanchard, production supervisor BARBARA RIES BARBARA 35 Fine-Tuning a Blood Pressure Elizabeth Cowley, copy editor H H M I O NLINE Jennifer Donovan, education editor Regulator Patricia Foster, manager of publishing Jim Keeley, science editor Inside Back Cover Dean Trackman, copy editor 36 Medicine and Computing Converge in a New Career RCW Communication Design Inc., publication design Telephone (301) 215 8855 • Fax (301) 215 8863 • www.hhmi.org The Bulletin is published by the HHMI Office of Communications, 37 How Sperm Jump-Starts Robert A. Potter, director. the Embryo © 2001 Howard Hughes Medical Institute LETTERS TO THE EDITOR We invite your comments. Send your letters via e-mail to 38 ‘First Light’ Gives [email protected] or regular mail to Letters, Office of Communications, Howard Hughes Medical Institute, 4000 Jones D.C. Students a Bridge Road, Chevy Chase, MD 20815-6789. We reserve the right to edit for space and clarity. Please also include your name, address Second Chance to (e-mail or postal) and phone number. Discover Science The opinions, beliefs and viewpoints expressed by authors 37 in the HHMI Bulletin do not necessarily reflect the opinions, beliefs and viewpoints or official policies of the Howard Hughes Medical Institute. N O T A B E N E

the 2000 Premio Phoenix-Anni Verdi HHMI President Thomas R. Cech, three award for genetic research from Italy. Thomas M. Jessell, an HHMI investiga- HHMI investigators and two members of tor at Columbia University College of the HHMI Scientific Review Board (SRB) Physicians and Surgeons, received the were elected to the Institute of Medicine Sean B. Carroll, an HHMI investigator at Paul Jansen Prize in Advanced (IOM) of the National Academy of the University of Wisconsin–Madison, Biotechnology and Medicine from the Sciences. Investigators Günter Blobel, received the Herbert W. Dickerman Rutgers University Center for Advanced The Rockefeller University; Peter S. Kim, Award from the Wadsworth Center of Biotechnology and Medicine. Whitehead Institute for Biomedical the New York State Department of Research; and Huda Y. Zoghbi, Baylor Health for his contributions to biomed- College of Medicine, will join the IOM, ical research. Susan L. Lindquist, an HHMI investiga- as will SRB members Steven E. Hyman, tor at The University of Chicago, National Institute of Mental Health, and received the Novartis-Drew Award in Thomas J. Kelly, The Johns Hopkins Steven F. Dowdy, an HHMI investigator Biomedical Research, which is given University School of Medicine. They at Washington University School of annually by Drew University and were among 60 new IOM members Medicine, received the first annual Novartis Pharmaceuticals. elected from the United States. Aventis Innovative Investigator Award for his work on protein transduction to deliver drugs, peptides and proteins into Nikola P. Pavletich, an HHMI investiga- HHMI investigators David E. Clapham, cells. tor at Memorial Sloan-Kettering Cancer Children’s Hospital, Boston; Mark M. Center, was named one of “20 Young Davis, Stanford University School of Scientists to Watch” in Discover maga- Medicine; Randy W. Schekman, Paula K. Frazer, a high school science zine’s 20th-anniversary issue. University of California, Berkeley; Paul teacher and member of the curriculum de - W. Sternberg, California Institute of velopment team of the HHMI-supported Technology; and Joseph S. Takahashi, Science Education Partnership at the Fred Charles F. Stevens, an HHMI investigator Northwestern University, were elected to Hutchinson Cancer Research Center in at The Salk Institute, received the 2000 the American Academy of Arts and Seattle, won a Presidential Award for Karl Spencer Lashley Award from the Sciences. The honorary society recognizes Excellence in Science and Mathematics American Philosophical Society for his achievement in the sciences, arts and Teaching. The annual awards are admin- research into the cellular and molecular humanities. istered and funded by the National mechanisms of synaptic plasticity. Science Foundation.

Margaret Andrews, a third-grade teacher Jack W. Szostak, an HHMI investigator in New Haven, Connecticut, and found- Jeffrey M. Friedman, an HHMI investi- at Massachusetts General Hospital, ing member of the HHMI Steering gator at The Rockefeller University, received the 2000 Genetics Society of Committee at the Yale Peabody Museum, received the 2000 Osborne Mendel America Medal for his contributions to received the 2000 Milken Educator Award from the American Society for genetics research. Award, a $25,000 prize. Nutritional Sciences and the 2000 Endocrinology Transatlantic Medal from the Society for Endocrinology of the David A. Williams, an HHMI investiga- Nancy C. Andrews, an HHMI investiga- United Kingdom, both for his research tor at Indiana University School of tor at Children’s Hospital, Boston, on the role of leptin in weight regulation. Medicine, received the 2000 William received the American Federation for Damesek Award from the American Medical Research Foundation’s 2000 Society of Hematology. The prize recog- Outstanding Investigator Award in Basic David L. Garbers, an HHMI investigator nizes his contributions to the field of Science for her work on the genetics of at the University of Texas Southwestern retroviral-mediated gene transfer and iron transport. Medical Center at Dallas, won the Edwin human gene therapy. B. Astwood Award, presented annually by the Endocrine Society for research in Mario R. Capecchi, an HHMI investiga- endocrinology. tor at the University of Utah, received the 2001 Jimenez-Diaz Prize from Spain and

HHMI BULLETIN 2 M A Y 2 0 0 1 KAY CHERNUSH KAY

THE OTHER GENOME RACE

ecently, two teams raced to complete their long-awaited Smelling the World and Blazing a publications about the human genome. One included sev- Genetic Trail—have also been Reral prominent institutions, led by the National Institutes adapted for the Web and are of Health (NIH). The other was a single Maryland-based organi- among the most popular features zation working on its own version of the genome publication. on HHMI’s site, www.hhmi.org. Both teams knew their work would be read widely, and they The latest volume, once again looked forward to making a splash among both scientists and edited by Maya Pines, includes the public. stories on how geneticists are Do I refer to the publication of the human DNA sequence in using “microarrayers” to analyze Science and Nature this past February? Of course not; you multiple genes simultaneously, already know about that. Instead, I’m referring to two related how studies of the cell-division cycle in yeast are helping us educational publications that will help students and the public understand cancer in humans and how genetic analysis of mice understand why the historic genome papers have caused so much could lead to better treatment of human diseases ranging from excitement. HHMI was among the supporters of the first publi- obesity to drug addiction. As usual, there are “how-to” features cation—a multimedia kit, actually—called The Human Genome and treats such as stories about drunken flies and socially inept Project: Exploring Our Molecular Selves. HHMI also produced worms that teach us about human behavior. There’s also a poster the second publication, The Genes We Share with Yeast, Flies, that illustrates the similarity across species of genes that have Worms, and Mice: New Clues to Human Health and Disease. been implicated in human diseases. Both efforts illustrate our commitment not only to extending the Recently, HHMI compiled the previous titles into a single vol- frontiers of biomedical research but also to sharing the discoveries ume, Exploring the Biomedical Revolution, which it is distribut- of HHMI investigators and other scientists with a wider audience. ing below cost through the Johns Hopkins University Press The multimedia kit, produced by the National Human (www.press.jhu.edu). The Genes We Share and those titles that Genome Research Institute of the NIH, features a video docu- remain in stock are available for free from the HHMI Web site, mentary, an interactive CD-ROM, a poster and a booklet. The as are other publications, videos and Web features on topics materials explain in nontechnical language what scientists have ranging from laboratory safety to undergraduate science educa- been learning about genetics and how their work is beginning to tion. A series of “Virtual Labs,” for example, enables students be applied in gene-based medicine and other advances. Teachers to search for genes, probe the nervous system or assay antibodies can order the kits for free from a Web site (www.nhgri.nih.gov/ while online. A new Web animation shows how genes interact to educationkit) that also offers animations, a teacher’s guide and guide the biological rhythms that cause us to sleep and wake, a other resources. HHMI sponsored the effort with the NIH, the topic explored this past December at our annual Holiday U.S. Department of Energy, the Pharmaceutical Research and Lectures on Science for high school students. Visitors to the Web Manufacturers of America, Nature, Science and the American site can also sign up for free copies of this magazine and for an Society of Human Genetics. online news service. These are but a few examples of our efforts The second project, The Genes We Share, is the latest in a to enhance science education from the earliest grades through series of clearly written, beautifully illustrated scientific publica- postgraduate training, the major focus of HHMI’s $100-million- tions that HHMI has prepared over the years for a general a-year grants program. audience. Teachers across the country have ordered thousands of Celebrated events like the publication of the human genome classroom sets of the free publications, often using them as sup- papers remind us that the rapid pace of biological discovery has plements to textbooks. Two of the titles—Seeing, Hearing, and an impact on society that extends far beyond the world of sci- ence. At HHMI, we consider it our responsibility not only to propel those discoveries but also to explain them to those out- side our laboratories. We want young people, especially, to understand how the research of HHMI investigators and others is changing their world. We hope that our outreach efforts will inspire at least some of them to come join us and make great dis- coveries of their own.

Thomas R. Cech President, Howard Hughes Medical Institute WILLIAM K. GEIGER WILLIAM K. HHMI BULLETIN 3 M A Y 2 0 0 1 UP FRONT

The Human Genome Goes to High School The National Human Genome Research Institute (NHGRI) of the National Institutes of Health has begun distribut- ing a new kit that will help high school teachers explain to students why the recent publication of the human genome was such a milestone. The kit consists of an interactive CD-ROM, a 16-minute videotape, a booklet and a poster, all produced by NHGRI with support from HHMI, the U.S. Department of Energy, the Pharmaceutical Research and Manufacturers of America, the American Society of Human Genetics and the jour- nals Nature and Science. The CD-ROM enables users to click on a particular year—starting with 1859, Two friends can look different and still share 99.9 when Charles Darwin published On the percent of their genes, the video from the kit explains. Origin of Species—and read a synopsis of an important related event, such as the first cloning of an animal gene in 1973. Each image links to more detailed information, so teachers can tailor the material for students at different levels. The CD-ROM also includes substantial material on ethical and social issues, such as how law enforcement officials, employers and insurance companies might use genetic information. The kit encourages teachers to allow the diver- gent opinions of their students to be heard on these issues. “Avoid seeking consensus on all issues,” it advises. Teachers can order the free kit online from NHGRI at www.nhgri.nih.gov/ educationkit. H Anne Haddad

A scrolling timeline on a CD-ROM tracks the history of genetics from Darwin and Mendel to today and tomorrow. The CD includes colorful animations of the process of making proteins in a cell.

HHMI BULLETIN 4 APRIL 2001 “We've read all the letters in the book of human life,” says James Watson, codiscoverer of the structure of DNA. “Now we're trying to put the letters together into words and the words into sentences.” Other scenes from the kit’s video include scientists working in DNA sequencing laboratories and close-ups of the human genome’s “products,” such as a crawling baby. WILLIAM K. GEIGER

The kit contains an interactive CD-ROM, a video, a poster and a booklet on genetics in medicine. UP FRONT Bringing Biology’s Models to Wall Street and Beyond A protein or DNA molecule is a won- systems.” For example, the oscillations The work requires dexterity in the use drous thing, a microscopic machine of chemical bonds may be extremely of mathematical tools and computational whose function is entwined with its rapid, whereas the actual adoption of a methods to analyze highly complex sys- structure. The static structure alone, specific three-dimensional protein struc- tems of multiple variables. Her students however, contains limited information, ture by a string of amino acids may have found success in far-flung fields just as a photograph of a car engine only occur at a relative snail’s pace. One way because those same tools and methods, hints at the engine’s function. The photo- she has successfully attacked the prob- and a comfort with mathematics, are graph needs to be replaced by a motion lem is by determining which factors widely applicable to systems outside picture. In the same way, Tamar Schlick must be addressed in scrupulous detail biology. “Having this background and is moving beyond biology’s static images over short periods of time (10–15 seconds) training is a great advantage,” says Bin to produce models and simulations that and which can be safely checked after Li, the chairman and chief executive reveal a biomolecule’s dynamic behavior. long stretches. Through her use of highly officer of Tradetrek.com, an investment An HHMI investigator who is also a efficient mathematical methods and her service on the Web. Li, who has a doc- professor of chemistry, mathematics and understanding of how to ask the most torate in physics, joined Schlick’s group computer science at New York University fruitful questions first, Schlick makes the in 1992 as a postdoctoral fellow; his (NYU), as well as a professor of bio- problem of molecular dynamics molecular dynamics work included study chemistry at NYU’s Medical Center, approachable. of the “supercoiling” of DNA. His first Schlick builds bridges throughout sci- ence. Her worldview has informed the lives of her students, some of whom have applied her training to ventures quite dis- tant from biology. Some academicians still frown upon the graduate or postdoctoral student who makes a career outside the ivy walls. The frown deepens for those whose paths take them away even from industries, such as pharmaceuticals or biotechnolo- gy, that relate directly to academic biological research. Several of Schlick’s students have found lives on Wall Street and in nonbiological high-technology fields—and Schlick thinks that is just fine. “Academia is not for everybody,” she says succinctly. When asked about students leaving science, she quickly responds that they merely left the academy, taking their science with them. Schlick works in the field of molecular dynamics, which aims to deduce evolution’s biochemical wisdom through models and simulations. How a protein folds or how portions of a DNA molecule work in concert to achieve a biological function are among her ques- tions. In Schlick’s efforts, time is always of the essence. “The problem in molecu- lar dynamics,” she says, “is one of very large spreads of timescales in biological

Some of the diverse researchers who train in Tamar Schlick’s HHMI laboratory at New York University go on to apply their skills in nonscientific settings.

HHMI BULLETIN 6 APRIL 2001 UP FRONT job after leaving the group in 1993 was such three-dimensional splines because evaluates performance and reliability for with Merrill Lynch. “Applied finance Schlick employed them to model DNA. AT&T’s Internet Protocol backbone,” was becoming a branch of science,” Li After leaving Merrill Lynch and spend- she says, referring to the system charged recalls, “and Wall Street started looking ing a stint with Swiss Bank Corporation, with transporting the Internet’s traffic for scientists who could crunch numbers, Li and colleagues started Tradetrek.com. flow. One benefit of her academic model financial securities and transac- Li says of scientists, “We tend to be objec- training, she says, is knowing how to for- tions and analyze risk. Experience in tive, quantitative and analytical.” That’s mulate the proper questions. “You need computational methods was very suitable a trinity that may prove as important to the ability to construct a model that cap- for that kind of work.” our times as liberty, equality, fraternity tures the problem,” she says. Similarly, Within six months of joining Merrill did to the French Revolution. Leonid Zaslavsky, a postdoctoral fellow Lynch, Li and physicist Eddy Van De Another Schlick-trained physicist, in Schlick’s group four years ago, took Wetering wrote a paper that circulated Guihua Zhang, followed Li to Merrill his knowledge of complex systems to privately within the financial industry Lynch and remains there as a vice presi- Microsoft Research. and became widely applied. The paper dent in fixed-income research. “Merrill Of course, most of Schlick’s students do explains how three-dimensional splines, Lynch thinks that my math, physics and opt for academia. Recent postdoc Daniel mathematical functions made up of numerical-analysis skills are helpful here Beard just took an academic job at the smaller functions smoothly joined togeth- to model interest rates in financial mar- University of Washington, where he er, could be used to model yield curves of kets,” he says. While working with received his doctorate in bioengineering. interest rates. Li knew how to work with Schlick, Zhang learned Monte Carlo sim- After doing what Schlick calls “beautiful work on modeling chromatin [the com- plex of proteins and nucleic acids that “Looking at the make up chromosomes],” Beard faced a decision. Like many other past Schlick postdocs, Beard interviewed with a couple big picture, I think of pharmaceutical companies. But, he says, “my feeling was that they wanted a narrow definition of computational biolo- it will help science gy.” So, like his predecessors, Beard decided to take a job where he saw an opportunity to apply his skills broadly— to have proponents which in his case happens to be academia. Schlick herself continues to look past the usual boundaries. In her laboratory a biochemist sits alongside a physicist, everywhere.” whose neighbor is a chemist, who shares a workstation with an applied mathe- ulations—a mathematical method, named matician. Schlick thinks that the local for the famous gambling capital, that New York City environment has played relates variables within complex systems at least a part in steering some of her by basically throwing the dice enough group members to finance, what with times to see a pattern. The Monte Carlo Wall Street just a short walk south of technique comes in handy in his financial NYU. work, although he notes one key differ- Some scientists may still argue that an ence between his new and old research exodus from academia is like a trade subjects: “Market models may be simpler deficit, with expensive training leaving than those for biology; there are far the country of science. Schlick believes, fewer variables!” however, that having scientists apply Gomathi Ramachandran’s work is their skills in new settings must be taken aimed at keeping the Internet chugging. as a positive. “They’re using what they Day traders playing the market may learned in a different way and developing sometimes think of the Web as some kind it further,” she says, “Looking at the big of badly behaved animal, a mule per- picture, I think it will help science to

CHRISTOPHER DENNEY haps, when a page refuses to load. have proponents everywhere.” Objective, Ramachandran, who has a doctorate in quantitative and analytical. H chemisty, learned mathematical tech- Steve Mirsky niques from Schlick that she now applies at AT&T. “I’m part of a group that

HHMI BULLETIN 7 APRIL 2001 UP FRONT

some late adolescents, the pairing might active himself in applying basic science to Shane Crotty have fueled a high-octane self-absorption. public health crises such as the AIDS For the gregarious Crotty, it only pro- pandemic. Instead, he found that he Has a Hot Paper pelled his curiosity about life writ both enjoyed the more reductionist, less stress- large and small. And what life loomed ful side of biology. Somewhat to his and a New larger than that of Nobel laureate David surprise, he also had discovered that he Baltimore, the current president of the liked to teach. So when the opportunity Biography,Too California Institute of Technology, who arose to capture, coordinate, write and was vindicated in a decade-long drama wrestle into shape the information for an Science may speak with the authority of concerning allegations of scientific fraud? online biology teaching course, a “hyper- age, but it often moves on the shoulders “I was taking a biography class and was textbook,” Crotty was its driving force. of youth. Shane Crotty, a 26-year-old told to write a 25-page assignment on a In this, too, he played the role of science HHMI predoctoral fellow at the serious topic,” Crotty recalls. “Since the writer, honing the same skills for explain- University of California, San Francisco core of Western literature has always ing everything from vaccines to viruses (UCSF), has been moving quickly. He just been conflict, I settled on the careers of that would later win him the praises of had a paper published in Nature E.O. Wilson [the evolutionary biologist book reviewers. Medicine on the discovery of a new at Harvard University] and David Looking back, the Kurt Vonnegut and mechanism that overwhelms RNA viruses, Baltimore.” Both were accessible from Tom Wolfe fan admits that his emerging and his biography of noted biologist Crotty’s Boston base, but Wilson was on profile cast no clinical shadows. “I knew David Baltimore is about to be pub- sabbatical, so it was Baltimore who got I wanted to be an academic scientist,” lished. Says Crotty, “It’s all very cool.” the call—or, more correctly, the e-mail. Crotty says. “And when I came to UCSF It also was, he concedes, all very Crotty’s scant knowledge of his chosen in 1996, I thought I wanted to study pro- unpredictable. As the son of an Air Force subject did not deter him. The interview tein evolution.” Perhaps he would have officer, Crotty loved to “hang out in with Baltimore went well, and using the stayed this course had not a virology nature,” yet it was the rhythms and wealth of information in MIT’s archives course taught by HHMI investigator atmosphere of the outdoors as much as for background, Crotty’s 25-page paper Donald Ganem and former Baltimore its biology that interested him. While tripled in size. It then doubled again postdoc Raul Andino intervened. “I was growing up in 11 different places from when, after nine more interviews, Crotty polishing the book at that point and Guam to New Mexico did nurture his had enough primary material to make it wanted to make sure what I was saying appreciation for natural diversity, it did about viruses was correct,” Crotty says. not create an irresistible attraction to “I realized that I That mundane task soon yielded to an fluorescent lighting and microscopes. epiphany: “I realized that I liked viruses. Indeed, he might have become a writer They are incredibly clever and they break had not a persistent high school chem- liked viruses.They the standard rules of biology.” As he istry teacher insisted that Crotty apply learned more about their strange para- for the National Science Foundation’s are incredibly clever sitic behavior, the tricks they use to Young Scholars Program. invade a host cell and take over its repro- “I blew it off at first,” Crotty recalls, ductive machinery and the novel health preferring the challenges of his creative- and they break the problems they pose, Crotty also realized writing elective. In what would be the something else. Outwitting such clever first of several turning points in his standard rules of adversaries was an appealing scientific young life, however, Crotty not only problem in its own right, but the chance applied to and qualified for the program, to prevent disease offered satisfaction of he also landed a job studying color vision biology.” a different sort. “I decided I would need in sharks in a laboratory on Catalina something to get me out of bed in the Island, off the coast of southern morning.” California. “I didn’t accomplish any- his thesis. Good fortune and good strate- Hepatitis C sufferers may one day be thing,” he recalls, “but I did learn what gy then converged. Crotty chose Alan glad he made that choice. For as part of that life was like.” And, he says, smiling Lightman, author of Einstein’s Dream, as a collaboration with Andino and at the more spartan research space of a his thesis adviser. “Lightman had been Pennsylvania State University researcher UCSF graduate student, “the lab on the the only person at MIT to give me a B, Craig Cameron, Crotty helped determine island was gorgeous.” so I figured I had something to learn how ribavirin, a drug used to treat the The chance to do research right away from him,” Crotty says. In the end, that disease, works—and why it sometimes lured him to the Massachusetts Institute something included how to secure a pub- doesn’t. “Until now,” Crotty says, “we of Technology in 1992. Armed with his lishing contract. didn’t have a good idea why only now twin passions—writing and biolo- The chance to probe Baltimore’s life one-third of patients responded to treat- gy—he enrolled as a double major. For and mind did not stir Crotty to become ment.” One theory suggested that

HHMI BULLETIN 8 MAY 2001 UP FRONT BARBARA RIES

Shane Crotty is pursuing his twin passions—writing and virology. viral cultures in petri dishes, more and drugs that use mutagenesis as a strategy more viral mutations occurred. Normally, to destroy other RNA viruses. viruses use their ability to mutate as a The importance of the work is not lost ribavirin killed RNA viruses, those that way to survive. Ribavirin turned this tac- on Crotty, who, lifting samples from his use RNA as their genetic material, by tic on its head, forcing the viruses to array of petri dishes, proudly traces the blocking enzyme synthesis. “But this mutate so often that they would self- viral death march. This was cool stuff, he wasn’t convincing. We knew that destruct. Called error catastrophe, the admits. “But,” he adds, “I have so much ribavirin impeded nucleotide enzymes mechanism is not new, but it had never more to learn, particularly about without any antiviral effect.” Crotty and before been demonstrated in an available immunology.” The next stop on that his colleagues also knew, however, that a drug. Not surprisingly, two pharmaceuti- quest is the laboratory of viral immunol- ribavirin nucleotide so closely resembles a cal companies are already using the ogy expert Rafi Ahmed at Emory viral nucleotide that it can trick the virus results to develop a more effective form University. “You know, we don’t really into mistakenly inserting ribavirin into of ribavirin, which also is used to treat know how to make good vaccines,” newly formed copies of its RNA genome. severe respiratory syncytial virus infec- Crotty says. If past is prelude, Crotty may What happened next was a surprise. As tions in newborns. Equally important, the help close the gap, smiling all the way. H Crotty added more and more drug to findings might help researchers discover Jeff Miller

HHMI BULLETIN 9 MAY 2001 PERSPECTIVE

Genetically Modified Crops

How They Appear to Geneticists— ease world hunger and other problems. and to Others We have a responsibility to share our expertise with the public—and to listen By Daphne Preuss carefully to what the public is really say- ing. One often hears, for example, that

There’s a famous New Yorker magazine genetically modified foods are inherently DAPHNE PREUSS cover depicting a New Yorker’s view of dangerous because they are “man-made.” the world, in which little except prairie People perceive these plants to be unnat- exists between Manhattan and California. ural, unlike “natural” plants developed In the same way, some nonscientists view through conventional methods. Rather Arabidopsis thaliana great discoveries as suddenly appearing than make light of this distinction, I’ve on the landscape of history. Penicillin! A worked with scientific organizations and gy that enables us to home in on a few polio vaccine! They do not see the twists even members of Congress to provide specific genes and leave everything else in the road along the way. some historical context about what plant alone. It is now quite a straightforward So it is in the public debate over geneti- science really involves. process to identify a gene that performs a cally modified foods. Most scientists, All traditional plant breeding is a ver- desirable function and insert it into a especially plant scientists like myself, view sion of genetic modification. As long as plant. It is also much easier to test these new organisms as part of a scientific 10,000 years ago, people started cultivat- whether this altered gene behaved as continuum that reaches back to ancient ing wheat and potatoes, making hybrids predicted instead of sorting through thou- times. Genetically modified corn, for and selecting varieties that tasted better, sands of new plants without knowing instance, is a cousin to the corn that was were bigger, resisted disease and so forth. what happened inside them. Easier, and on our dinner table a decade ago—a Maize would not exist if early farmers safer as well. product that was created through had not undertaken breeding methods to One health concern voiced about conventional breeding methods. Many produce mutations of a wild food called genetically modified crops is that toxins opponents, on the other hand, see geneti- teosinte. In fact, maize cannot reproduce or allergens might be introduced into a cally modified foods as threats that on its own without human intervention. plant during genetic manipulation. appeared suddenly on the prairie. Overall, human manipulation in the Scientists know how to test for the pres- This poses a challenge for those of us in breeding of plants and animals has been ence of toxins, however, and a regulato- the scientific community who believe so extensive that almost every product in ry network exists to ensure that the test- these new foods have great potential to our supermarkets today resulted from ing is done correctly. Allergens pose a genetic alteration. During the past century, different challenge, since it can be diffi- these breeding techniques have only inten- cult to test for a potential allergen that sified and become more sophisticated. affects only a few people. Yet the odds Companies and farmers generally focus of an allergen emerging are higher when on a few traits, such as a plant’s hardiness 25,000 genes are combined through or the size of its fruit. Traditional breed- conventional breeding than when only ers scramble thousands of genes from one gene or a few are relocated. parent plants in an effort to produce off- A big environmental concern is that spring with desired traits. It’s a process genetically modified plants might that is highly random from a genetic cross-pollinate with native species or standpoint, since there is little control unintentionally harm insects and other over the genes involved. Yet, because it is animals. These issues also exist for con- MARK SEGAL widely practiced, this random mixing of ventionally bred plants, however, and genes evokes little concern about the pos- organizations such as the Environmental sibility of creating organisms that are Protection Agency have established reg- harmful to health or the environment. Daphne Preuss ulations to monitor the risks and to As a geneticist, I find this approach assess new crops. It is essential that the much more troubling than new technolo- scientific and regulatory communities

HHMI BULLETIN 10 APRIL 2001 look at each plant on a case-by-case sure from international environmental basis and exercise the necessary over- groups. I now doubt whether our work sight to protect the public and ensure will ever see the light of day. Like many safety. critics, I wish it were possible to do all The potential benefits of genetically farming organically, using little or no modified foods are tremendous, and not chemical fertilizers or pesticides; in the only as regards improved nutritional future, new transgenic crops may make value and taste, or stronger and more this possible. “Organic farming” as now abundant crops. New plants might also practiced by many subsistence farmers in reduce the demand for water and harm- Mexico typically means poor people ful pesticides. By genetically harnessing HECTOR X. AMEZQUITA using outdated methods because they the natural chemicals in plants, scientists have no alternative. It is quite distressing, might create varieties that detoxify soil for example, that even today, children contaminants or produce the materials miss school because they must help their for medications, plastics, paper or fuel. parents to pick weeds by hand. Those of us who work with genes every Luis Herrera-Estrella Our team has filed for patents on the day in the laboratory can easily forget plants we’ve developed, and we plan to how menacing “genetic engineering” can dant supermarkets. I detect little enforce the patents in developed coun- sound to the public, especially when it appreciation for the fact that the average tries that can afford to contribute to our comes to food. As scientists, we under- Mexican farmer has just five acres of continuing research. Our real goal, how- stand intuitively that genetically modified land on which to grow the staple crop of ever, is to provide the plants for free to foods did not just suddenly appear on the maize—hardly enough land even without small farmers in Mexico and elsewhere. landscape between New York and the marginal soils, insufficient water, In the long run, our biggest obstacle California. As the debate over these foods abundant pests, plant diseases and other may lie not with publicized protests but continues, we need to do a better job of problems that are common here. with the lack of interest from others who explaining this landscape to the public. Transgenic crops offer a way to might assist us. Just as pharmaceutical We must make clear that we, as fellow improve yields dramatically while easing companies have been slow to develop citizens, want this new technology to be concerns about related matters such as vaccines and medicines for tropical dis- used responsibly, for the benefit of people pollution. Nearly 20 years ago, I worked eases, so have agricultural companies everywhere. on a team that transferred an antibiotic- paid little attention to the needs of small resistance gene into a plant, thereby cre- farmers in developing countries. It’s also Daphne Preuss, an HHMI investigator at ating the world’s first plant modified difficult for scientists like me to find the The University of Chicago, works with through genetic engineering. We knew venture capital or research support that Arabidopsis thaliana and other plants to that these experiments could have a great is common in richer countries. study how cells interact to regulate impact on agriculture, and, sure enough, As a scientist who has dedicated his life growth and development. scientists have subsequently used genetic to this problem, I know that plant genet- techniques to develop a variety of ic engineering offers a powerful way to improved crops. provide more food for my country. I’d How They Might Help like to help make effective use of plant Countries Like Mexico My recent research has focused on developing plant varieties that can grow genetic engineering and agree completely By Luis Herrera-Estrella in the acidic soils that are prevalent in with the need to do so responsibly, tak- Mexico. Our team seeks to produce plant ing care to avoid environmental or health The controversy over genetically modi- varieties that are tolerant to toxic forms problems, if we ever face them. Such con- fied foods is having a big impact on of aluminum present in these soils and cerns, however, should be analyzed on scientists who want to produce more and that have a higher capacity to use soil the basis of solid scientific data, not sen- better food in countries such as Mexico. nutrients such as phosphate. We have timent. They should not paralyze us from My own efforts to conduct field trials of engineered a new variety of maize that making rational decisions about how sci- genetically modified maize have been releases high amounts of a natural chemi- ence can best be used to improve life for thwarted by foreign groups lobbying our cal called citrate, which latches on to and people in my country and elsewhere who government. The controversy has slowed blocks the toxic forms of aluminum. The need this technology the most. our funding and made it harder for us to citrate also releases phosphate from the work with small farmers. soil, helping the plants grow and reduc- Luis Herrera-Estrella, an HHMI interna- When I listen to critics in Europe and ing the need for fertilizers. tional research scholar, is a professor and the United States, I sometimes get the This new maize has the potential to head of the plant genetic engineering feeling that they want us to keep living as significantly increase the yields for farm- department at the Center for Research if we’re in a museum that they can visit ers, but the government has not granted and Advanced Studies in Irapuato, before they return home to their abun- us permits for field tests because of pres- Mexico.

HHMI BULLETIN 11 APRIL 2001 MUSCLEHEADS Our faces have 44 muscles, most of which contract in a single way. Some muscles, such as those in our foreheads, can move in several ways. Scientists have defined these various movements in “facial action codes,” which they program computers to recognize. From Paul Ekman & Wallace Friesen, The Facial Action Coding System, originally published by Consulting Psychology Press, 1978. Facing the TRUTH A New Tool to Analyze Our Expressions

By Nancy Ross-Flanigan curled lip, a furrowed brow—sometimes even a small A change in expression can reveal far more than words. We all like to think we can read people’s faces for signs of their true emotions. Now, a computer program can analyze images of faces as accurately as trained professionals.

What’s more, it does so faster. Working frame by frame, the most proficient human experts take an hour to code the 1,800 frames contained in one minute of video images, a job that the computer program does in only five minutes. A team led by HHMI investigator Terrence Sejnowski reported the

HHMI BULLETIN 13 MAY 2001 MARK HARMEL

feat in the March 1999 issue of the jour- nal Psychophysiology. The automated system, which has been Sejnowski is most interested in using improved since the article appeared, could be a boon for behavioral studies. Scientists have already found ways, for example, to the system to explore information distinguish false facial expressions of emo- tion from genuine ones. In depressed individuals, they’ve also discovered differ- ences between the facial signals of suicidal processing in the human brain. He likes and nonsuicidal patients. Such research relies on a coding system developed in the 1970s by Paul Ekman of the University of to think of the brain’s changing activity California, San Francisco, a coauthor of the Psychophysiology paper. Ekman’s Facial Action Coding System (FACS) patterns as “brain expressions,” similar breaks down facial expressions into 46 individual motions, or action units. Sejnowski’s team designed the computer in many ways to facial expressions. program to use the same coding system. Their challenge was to enable the program to recognize the minute facial movements upon which the coding system is based. who performed with only 73.7 percent A computer that accurately reads facial Other researchers had come up with dif- accuracy after receiving less than an hour expressions could result in a better lie detec- ferent computerized approaches for ana- of practice in recognizing and coding tor, which is why the CIA is funding the lyzing facial motion, but all had limita- action units. The coding process involves joint project. But Sejnowski sees other pos- tions, says Sejnowski, who is director identifying and marking sequences of sible commercial applications as well. of the Computational Neurobiology frames in which an individual facial “This software could very well end up Laboratory at The Salk Institute for expression begins, peaks and ends. A being part of everybody’s computer,” he Biological Studies in La Jolla, California, minute of video can contain several hun- says. “One of the goals of computer sci- and a professor of biology at the dred action units to recognize and code. ence is to have computers interact with University of California, San Diego In the work reported in Psychophysiology, us in the same way we interact with other (UCSD). A technique called feature-based the researchers taught the computer pro- human beings. We’re beginning to see analysis, for example, measures variables gram to recognize 6 of the 46 action programs that can recognize speech.” such as the degree of skin wrinkling at var- units. Since then, the program has mas- But humans use more than speech recog- ious points on the face. “The trouble,” tered six more and, by incorporating new nition when they communicate with each Sejnowski explains, “is that some people image-analysis methods developed in other, he explains. In face-to-face conver- don’t wrinkle at all and some wrinkle a lot. Sejnowski’s lab, the system’s performance sation, “you watch how a person reacts It depends on age and a lot of other fac- has risen to 95 percent accuracy. The to know whether they’ve understood tors, so it’s not always reliable.” additional work was published in the what you’ve said and how they feel His team—which included Ekman, October 1999 issue of IEEE Transactions about it.” Your desktop computer can’t Marian Stewart Bartlett of UCSD and on Pattern Analysis and Machine do that, so it doesn’t know when it has Joseph Hager of Network Information Intelligence. correctly interpreted your words or when Research Corp. in Salt Lake City—took Now the team is engaged in a friendly it has bungled the meaning. With this the best parts of three existing facial- “cooperative competition” with researchers software and a video camera mounted on motion-analysis systems and combined from Carnegie Mellon University and the your monitor, Sejnowski thinks your them. University of Pittsburgh who have devel- computer might someday read you as “We discovered that although each of oped a similar system. The two systems will well as your best friend does. the methods was imperfect, when we com- be tested on the same images to allow direct bined them the hybrid method performed comparisons of performance on individual about as well as the human expert, which images as well as overall accuracy. The Sejnowski and his team are engaged in a is at an accuracy of around 91 percent,” teams will then collaborate on a new friendly “cooperative competition” with Sejnowski says. The computer program system that incorporates the best features of other researchers, with whom they will did much better than human nonexperts, each. collaborate on improved systems.

HHMI BULLETIN 14 MAY 2001

Analyzing Our Expressions

BRIGHT LIGHTS, MOVING HEADS FAKE EXPRESSIONS

A computer system has to be taught to “see” someone’s furrowing brow or crinkly smile. Sejnowski and his team have drawn from diverse fields of science, such as artificial intelligence and neural networks, to handle this task. Among the many hurdles they face is head movements and varying light conditions. To overcome this, their system breaks down the images of faces into tiny units, measures the light in each dot, and then compares the mosaic to known facial patterns. It’s a process that resembles—but is far more primitive than—the way our brains make sense of light passing through the eye. In these photos, the smile on the left is false while the smile on the right is real.

BE VERY AFRAID Several facial cues suggest that someone is faking an expression, among them: If the outer part of your eyebrow goes up, • The muscle contractions on the left side of you’re probably afraid—although you may the face differ from those on the right side. just be feeling surprise. To determine • The expressions start and stop in a jerky manner. whether someone is truly afraid, like the • The person holds the expression for too long. man in this photo, Sejnowski’s team looks for several other facial actions that indicate Eye movements also provide information. fear. All of the following movements in the Someone looking downward may be sad, while upper part of the face may indicate fear, someone looking down or away is more likely feel- although some are also associated with ing shame, guilt or disgust. The sad look on this other emotions: man’s face is false. • Raising the upper eyelid to show the whites of the eyes • Raising the inner brow: Also may show sadness • Lowering the brow: Also may show anger or mental effort • Tightening the eyelid: Also may show anger or disgust

HHMI BULLETIN 16 MAY 2001 And speaking of best friends, the soft- ware could conceivably give robotic pets a leg up on the furry kind. In a project at A BETTER LIE DETECTOR UCSD, the researchers are integrating their system into the popular robotic dog No one has yet created an infallible tool to AIBO, developed by Sony Corp., with spot a liar. It’s only possible to measure a the goal of training the robo-pet to rec- person’s emotions and then determine ognize individual people and respond to whether these are consistent with the per- their emotions. For example, says son being truthful. That’s the idea behind Sejnowski, “AIBO might comfort you if you are upset or play with you if you are the polygraph, which measures increases in restless.” The eventual product could be sweating, heart rate and breathing rate that more than just a high-tech toy. With are associated with heightened emotion. recent research showing health benefits New technology that analyzes faces may from interacting with pets, an empathic improve on this classic “lie detector” by AIBO might be good medicine for people too ill or frail to care for living animals. revealing not only the presence of emotion Exciting as the commercial prospects but also the type of emotion. For example, a may be, Sejnowski says he’s most inter- man who is asked “Did you kill your wife?” ested in using the system to explore during a polygraph test might “fail” because information processing in the human he felt either anger or disgust—emotions brain. “In the recent work, we find that the best performance comes from a that cause similar physical reactions but method based on the way that single neu- have different implications for innocence or security clearances. Unfortunately, innocent rons filter visual images in the very first guilt. A facial analysis, on the other hand, people sometimes fail the tests, and auto- stage of processing in the visual cortex,” might distinguish between anger and dis- matic facial measurement systems are not he says. “The next step is to see whether gust, providing police with a valuable yet ready to take their place. or not some of the subsequent stages of processing in the visual system line up insight. Comprehensive systems are still at least with the methods that we’ve developed.” Polygraph tests are not normally admis- 5 to 10 years away, and they will need to be The new methods are also proving use- sible in courts of law in the United States, tested extensively before they can even be ful in analyzing brain images obtained but they are often used when both sides considered for use in the legal system, the through functional magnetic resonance agree in advance, such as for workplace workplace or elsewhere. imaging. Sejnowski likes to think of the brain’s changing activity patterns as “brain expressions,” similar in many ways to facial expressions. The goal of A GLIMPSE OF THE TRUTH his new work is to understand, by ana- True emotions often flash across a person’s face in less lyzing sequences of brain images, how different patterns of neural activity relate than a quarter of a second. A person feeling fear or dis- to particular tasks the brain is tackling or gust, for example, can cover up with a smile before thoughts that are flickering through it. others realize what happened. A big advantage of com- “The face expresses what’s going on in puters is that they can analyze videotapes to spot such the brain, but it’s only a pale reflection,” “microexpressions” more quickly and accurately. Even Sejnowski says. “Now we have the capabil- ity, with brain imaging, to actually look good actors find it difficult to prevent their faces from COURTESY OF PAULPHOTOS: EKMAN inside and see what’s going on in the per- revealing this moment of truth, especially if they are son’s mind while they’re experiencing an unprepared for the question. In this photo, the man’s emotion and making the facial expression.” smile is false.

HHMI BULLETIN 17 MAY 2001 cientific perceptions can some- times shift so rapidly that it is

difficult to remember an earlier BARBARA RIES reality. A decade ago, there SSwere no topographical images of DNA in its natural, watery environ- ment. What instead ruled the popular imagination, and to some extent the sci- entific one, was the double-helix icon and its elegant edifice of genes. This aes- thetic view, even when elaborated by flu- orescent staining images, said nothing about DNA’s tensile properties and other physical properties, or about its ability to unwind prior to replication at speeds of more than 8,000 revolutions per minute. Scientists knew, of course, that there must be physical forces at work, tiny parts and little motors that were work- ing together to drive all the molecular movement essential to replication and transcription. But such forces were hid- den and difficult to measure. Moreover, DNA molecules, although durable, were not unbreakable; they could not be probed and prodded by brute-force methods. To understand the mechanisms behind all the coiling, copying, snipping and splicing required a more subtle approach that did not interfere with the very activities researchers were trying to see and “feel.” Enter Carlos Bustamante, a self- described “patchwork biophysicist” with an insatiable curiosity about how biological machines work. In rapid suc- cession in the early 1990s, his team pro- duced both the first topographical images of DNA in water and the first measurements of DNA’s elasticity. Still, Touching the

HHMI BULLETIN 18 MAY 2001 the images of these double-stranded helix- lot, but not so much anymore,” says bine to form the cellular factory. es did little to explain something Bustamante, now a 49-year-old HHMI If the goal is lofty, at its core it remains a Bustamante had questioned in his earlier investigator and professor of biochemistry mechanistic one—and not so different, at work: Just how elastic is DNA anyway, and molecular biology at the University of least in principle, from Bustamante’s child- and why should anyone care? California, Berkeley. As the son of a physi- hood determination to take apart and The first question was fundamental, if cian, Bustamante understands the need to rebuild toy cars. “It’s the same in biology,” unglamorous. It has long been thought that weigh the worth of research by its clinical he says. “I like to break things down to DNA must have a high degree of elasticity. potential. As a practical man, however, he understand their controls and their parts After all, before replication the molecule realizes that such is not immediately obvi- and then put them back together—with, I wraps itself around nucleosomes—those ous amid arcane mathematical equations. hope, nothing left over.” structural supports made of proteins— Yet, he is not worried about his work’s This need to reason and quantify rever- packs itself and folds into the highly bent berates throughout Bustamante’s life and structure of chromosomes. With typical “I like to break things career. At age 12, growing up in Peru, he directness, Bustamante and his colleagues built rockets and propelled them with the anchored one end of a DNA molecule to down to understand explosive combination of potassium per- glass and attached a bead of known mass their controls and their chlorate, sucrose and sulfuric acid. By age to the other. Gravity then did the rest. “It 16, he was working in his own home labo- was crude,” he says. “But, for the first parts and then put them ratory, studying the behavior of paramecia. time, we were able to get some measure- By his mid-20s, he was an international ment of the force required to extend the back together— Fulbright scholar at UC Berkeley with a molecule from its springlike resting state.” background in mathematics and physics Next, they tried magnetic beads. As with, I hope, nothing and a lasting love for microscopes. “Even reported in Science in November 1992, the left over.” as a young boy,” he says, “I was always beads moved in conjunction with external trying to predict outcomes and to construct magnets, movement that Bustamante’s ultimate relevance. For apart from the reasons for what I was seeing through the team was able to follow with a video intriguing discoveries his team has made lens.” camera. The researchers were also able about protein fatigue in muscle, If Bustamante’s instincts and interests measure the force needed to stretch out, or Bustamante knows that deciphering how seemed to make him an ideal candidate to extend, the single DNA molecule. “The the molecular machines of the cell work study the structure and forces behind mo- fact that we could measure the elasticity will reveal deeper truths about biology. lecular activity, however, they were not a was probably less important than the fact “For example, we now know a lot of the guarantee. “After I finished my scholarship that we had opened the door to inves- details about how the parts of the machin- at Berkeley, I wanted to go back to Peru tigating and manipulating individual ery work during DNA replication, and we and thought the best way to do that was to molecules,” he says. “Later, we learned are learning how chemical energy is con- become more of a theorist,” he says. But that there was a difference in elasticity verted into movement and how efficient challenged by his thesis adviser to build a between single- and double-stranded DNA these motors are,” he says. “Once we have machine that tested his theories of optical and that we could use this difference as the the machine, we can theorize and test why activity—a machine he built and used suc- basis for new biochemical tests.” it is constructed that way.” The next step, cessfully—Bustamante stayed. And as Interesting, to be sure, from a purely he says, is to understand the relationship improved technology and career opportu- physical point of view. But biologically sig- between these individual molecular nities converged in the 1980s, the curious nificant? “It’s a question I used to hear a machines and the many others that com- biochemistry and physics student gradually

One Molecule at a Time By Jeff Miller “It’s amazing. You can measure the bursts of activity as the polymerase loads

also speeded the development of related techniques, such as optical tweezers, which use the conservation of light’s momentum to trap tiny objects and manipulate individual molecules. Indeed, it was the tweezers’ ability to capture, move and stretch molecules and measure tiny changes in their fluctuating environ- ment that enabled Bustamante and his team to determine the difference in elas- ticity between single- and double-stranded DNA. The trapping action occurs when the tightly focused light of a single laser,

GEORGE EADE sent through a microscope, captures the desired target. Moving the light moves the target, without any need to actually touch the biological sample. The change in momentum as light spills from the trap provides both the trapping force and a way to measure this force. This “optical trap” reveals the dynamics of DNA’s replication molecular machinery. With such refined techniques at their Scientists use the device to measure the force that’s produced as DNA is converted disposal, Bustamante and his colleagues from its single-stranded form (right) to its double-stranded form (left). Two beads hold set about putting DNA fragments to vari- the DNA in place. The bead on the left rests atop a pipette, while the bead on the ous microscopy and trapping tests. In right sits in a laser beam. The DNA stretches between the two beads, producing a some cases, such as that reported last year measurable amount of force. When the polymerase molecule in the middle adds base in Nature, they have introduced the pairs to the DNA, this force changes, causing the bead on the right to move slightly enzyme DNA polymerase to a single within the laser beam. Researchers can measure this movement optically. The more the strand of DNA and “watched” and bead moves, the more force the DNA produced. Knowing the amount of force given measured its motion as it helped the off at each moment helps scientists understand the “mechanics” of DNA synthesis. strand pair off with the proper bases and Adapted from Fig. 1a, Nature 404:103, 2000 © Macmillan Magazines Ltd. rebuild itself into double-stranded DNA. “It’s amazing,” Bustamante says. “You can measure the bursts of activity as the turned his sights to the biophysics of light reflected off the back of the polymerase loads onto the chain, repli- molecular movement and to its essential cantilever to record and translate it into a cates and falls off. You can actually follow problem: How could you see, feel and three-dimensional image of the scanned biochemical processes by a single mole- measure what was going on? surface. In the late 1980s, while at the cule in real time.” At a catalysis rate of Atomic force microscopy (AFM), University of New Mexico, Bustamante more than 100 bases per second, it does invented by physicists in 1986, gave him and his colleagues had been among the not take long for the rubber-band shape of both sight and insight. “AFM works by first to use new DNA fluorescence stain- single-stranded DNA to be transformed touching,” Bustamante says, “much like a ing techniques and wire electrodes to into the distinctive “garden hose” of its blind person uses Braille.” In short, a can- induce and study molecular movement double-stranded cousin. tilever with a sharp tip, often made of under the microscope—in real time. AFM “Whenever we study these biochemical silicon nitride, is scanned over a surface at offered better visuals, something he had processes at the single-molecule level, we a constant force or height. The soft physi- proved with his eye-opening topographi- find that the molecules have a random, cal contact causes the cantilever to bend cal images of DNA, but it had the poten- almost chaotic behavior that is far from to accommodate changes in topography, tial to offer more. the average, smooth picture we get when the result of a repulsive atomic force that Exploiting this potential required con- we study whole ensembles of the mole- arises between atoms in the tip and atoms tinuing improvements not only in AFM cules by traditional ‘bulk’ methods,” in the sample. As the tip moves, feedback but in fluorescence staining, which uses Bustamante explains. “Inside the cell, mechanisms employing lasers and photo- special dyes to make parts of the cell many of these fundamental processes are detectors measure the difference in the nucleus visible under the microscope. It carried out by only a few molecules at a

HHMI BULLETIN 20 MAY 2001 onto the chain, replicates and falls off. You can actually follow biochemical processes by a single molecule in real time.”

time. I believe we’ll get a more realistic essential to muscle function. Apart from and his team are learning more about the view of the cell’s inner workings if we can learning the tension incorporated into its many molecular machines and testing follow the work of each molecule individ- coiled shape, the researchers have found their own predictions about why they ually.” that repeated unfolding induces a kind of work in the manner they do. At the same In other experiments, Bustamante uses molecular fatigue. “The protein recovers time, they are tinkering with AFM in pur- different polymerases to investigate how and refolds after a few minutes,” he says. suit of the day when they can achieve much of the transcription process is con- “We are now trying to find out the nanometer-scale resolution of biological trolled by the dynamics of the enzymes advantages of this delay.” The answer samples in liquid, a resolution now pos- translocating over the DNA, pairing new may ultimately offer some clues to fore- sible only if the desired samples are in a nucleotides with their proper bases in the stalling heart failure and the effects of vacuum. As for maintaining his own high- matching RNA. And in still different Duchenne’s muscular dystrophy, two yield enthusiasm, Bustamante does not experiments, his team has used laser conditions where titin—and muscle con- worry. “Loving science is the engine for tweezers to stretch and unfold the giant traction—are highly compromised. doing it. I am self-propelled.” protein molecule known as titin, which is With each new experiment, Bustamante

ROLES and MODELS Carlos Bustamante remembers the moment well. It was a sum- Nor is Bustamante’s symbolic signifi- mer morning in 1964, and he was going through some of his cance limited to Hispanic students. father’s books. He noticed one that happened to be written by Trained in both physics and biochem- ©THE NOBEL FOUNDATION a Spanish scientist, Santiago Ramón y Cajal, who received the istry, he has carved out as distinctive a Nobel Prize in 1906 for his work in determining the structure research career as curiosity, opportunity of the nervous system. and technology allowed. “There was no “This was a major turning point in my life,” Bustamante clear pathway for me,” he says. “I came says. “I had a sense of inadequacy because the only scientists I to biophysics haphazardly.” Now, in this Santiago Ramón y Cajal knew about until then had foreign names, which did not res- “new era of biophysics,” he advises nine onate to my Spanish ears.” biophysics graduate students in his laboratories in the physics Ramón y Cajal certainly could not have anticipated his future and biology departments at UC Berkeley and has helped design as a role model for an inquisitive teenage boy in Peru, but it is a curriculum that exposes physics majors to biology and vice a role that Bustamante has understood and accepted as he has versa, with mathematics courses as the common bond. built his own academic and research career. “I do not consider Says Bustamante with confidence, “These students are becom- myself an activist, but I am aware of what listening to me may ing the phenotype for the biophysicist of the future, the ones mean to Hispanic students,” says Bustamante, an HHMI inves- who will deal at a completely quantitative level with biological tigator at the University of California, Berkeley. “Many times, problems.” Moreover, these future scientists could be the van- they have come up to me after a lecture and expressed their joy guard in a transformation of biology from an organic to a syn- in hearing science spoken about with a Spanish accent.” thetic science. “It’s clear,” he explains, “that in time we will stop When he was teaching at the University of New Mexico in studying what is and start building what is not.” the mid-1980s, Bustamante inspired a generation of native In the meantime, Bustamante continues to hone his own Spanish-speaking students, many of whom were the first in teaching techniques. “I always have been in love with learning,” their families to attend college. To him, these students repre- he says, “so when I first started teaching, I assumed everyone sented the first link in what might become a family chain of else had the same feeling. I eventually learned that many people professional achievement. “In most cases,” he says, “the educa- are afraid, so I think it is important to offer equal parts of tional success of one child had a positive effect on the other enthusiasm and reassurance.” children in the family, who then sought some sort of profes- —JM sional degree or certificate of their own.” SOLVING BY DENNIS MEREDITH

Before Rick Lifton and his colleagues t’s an insidious, silent began studying hypertension at the mo- lecular level, most doctors viewed it as an impossibly intricate puzzle whose pieces killer that can surface consisted largely of environmental influ- ences such as diet and exercise. In recent years, however, Lifton’s group has made suddenly to trigger a series of important findings establishing the powerful role of genes—in particular, I mutations that alter salt metabolism—in heart attack, kidney this devastating disorder that affects one in four Americans. The change in perspective resulting from Lifton’s genetic studies, carried out failure or stroke. With by an energetic team of clinician- researchers at Yale’s Boyer Center for Molecular Medicine, is reverberating every heartbeat, chronic throughout the biomedical community. “Thanks to Lifton’s landmark research, hypertension is now in the mainstream of high blood pressure molecular medicine,” says Joseph L. Goldstein, professor and chair of molecular genetics at the University overworks the heart and of Texas Southwestern Medical Center and corecipient of the 1985 Nobel Prize in physiology or medi- distends arteries, slowly cine for his research on cholesterol metabolism. Goldstein also heads HHMI’s medical advisory board. It was, indeed, the prospect of causing them to thicken overturning conventional wisdom that tantalized Lifton 15 years ago and clog. But exactly when he emerged from a residency

how and why the Rick Lifton (left) studies hypertension with team disease arises has been member David Geller. a subject of confusion.

HHMI BULLETIN 22 MAY 2001 hypertension’s HAROLD SHAPIRO DEVELOPING the HOLISTIC SCIENTIST

Rick Lifton’s brightly lit maze of laboratories and studying it, he admits.“I think there are a lot of offices, arrayed along a gracefully curved corridor laboratories that operate more as factories,” he of Yale’s Boyer Center for Molecular Medicine, is a says. Among such labs, Lifton has observed two deceptively low-key place.The few sounds—the particular syndromes. delicate clink of glassware at lab benches, the click- “One is where the lab is built around a particu- ing of computer keys, the subtle murmur of con- lar technology, and that’s it. It’s like the old saying sultations over data—give little hint of the dynam- that to a child with a hammer, everything is a nail. ic discoveries emerging from within. This laboratory’s leaders say,‘We won’t think Lifton is naturally proud of those accomplish- about doing problems that can’t use this same ments, but he’s equally proud of the scientists he hammer and the same nail,’ ” he explains. mentors here, most of them physicians with purely “And secondly, there’s the phenomenon of team clinical backgrounds.These young scientists are science. In some areas, including genomics, it’s rel- mastering the full range of talents they’ll need to atively popular to develop, either within or across see their own projects through from start to finish labs, big consortiums in which you divide up the and to assume leadership roles in their fields. problem. As a result, one person will only do, say, Given Lifton’s holistic perspective, team members the analysis of linkage, and one person will only come away not only equipped to pin down a dis- do the physical mapping, and one person will only ease in the clinic but also capable of rigorously do the gene identification and mutation detec- analyzing its genetics and then figuring out how a tion.” genetic mutation causes disease. Such an approach may seem efficient, but ulti- “Most of the people trained in his lab have been mately it does not produce fully capable scientists, physicians who came here not even knowing how Lifton contends.“I think in the long run it takes to run a gel and then left as really good scientists,” away a lot of the zest of doing science—which is says Murat Gunel, a neurosurgeon who joined the driven by the fact that you’ve got an interesting lab eight years ago and is now establishing his own problem.The reason you want to do science is research group.“They learned to ask the key ques- that you’re passionate about solving problems.” tions that enable translation of basic research to Researchers with holistic training are also pre- answer clinical problems.” pared to adapt to changing scientific tools and to The need to master both the tools of the pro- lead the way in developing them.“Anyone work- fession and the strategy of using them to attack ing today who thinks that 10 years from now scientific questions was a lesson Lifton learned they’re going to be using the same tools is sadly early on.“I was fortunate to have some spectacu- mistaken,” Lifton warns. lar mentors who gave me extremely good training Ali Gharavi, a physician in the laboratory, rel- and insight into how to approach problems,” he ishes the environment Lifton has created.“There says, citing in particular Lawrence Kedes and are no walls, no barriers, in this lab. I walked in David Hogness, with whom he worked at and Rick said,‘Pick a project and you can work on Stanford. Just as those scientists encouraged him it.’ And having an M.D., I could identify certain to identify his own project and follow wherever it problems that were important in my field and try led, so Lifton does for the young scientists in his to address them.” own laboratory. For Murat Gunel as well, Lifton’s encourage- “I realized that to be successful in science, one ment has been crucial. needs to be intellectually flexible and not just “As I had to make the important choices, he wedded to one set of tools,” he says.“That’s not helped me and guided me,” Gunel says.“At those going to give an individual a broad perspective on times when I felt I was only going to be a science or the confidence to start their own lab.” mediocre scientist, it was Rick who kept pushing Many labs don’t allow young researchers to me, supporting me.” identify a disease and take full responsibility for —DM Rather than tackle the massive puzzle of hypertension in the entire population, Lifton at Boston’s Brigham and Women’s order lack receptors for low-density decided to narrow his Hospital pondering where best to lipoprotein and thus cannot remove this focus to genetic concentrate his energies. The young physi- form of cholesterol from the bloodstream cian-scientist was already well equipped led to a radically new molecular under- disorders affecting scientifically, having done graduate standing of the illness and set the stage for research in the Stanford laboratory of the multibillion-dollar market for choles- blood pressure. molecular biologist David Hogness. terol-lowering drugs. There, isolating genes in fruit flies, he “I figured the genetic approach might to look at the results. The autoradiogram learned new techniques of genetic manip- allow us to get our foot in the door in was unequivocal and clearly showed that ulation and analysis. He also established terms of understanding some of the the head of one gene had been fused to the an indefatigable, independent-minded fundamental pathways that affect blood body of the other. This resulted in abnor- research style, often working until three in pressure,” Lifton says. So he decided to mal regulation of a critical steroid the morning to chase down a result, grab- search for rare, single-gene forms of high hormone. These are the rare moments of bing a few hours’ sleep and then returning and low blood pressure, using them to discovery and insight that we thrive on.” to the bench at dawn to launch his quest gain clues to the overall pathways With this success under his belt, Lifton for the next piece of data. involved in blood pressure regulation. launched studies of every inherited form “I came out of residency and saw that Lifton recalls that there was also doubt of high or low blood pressure for which there were a lot of smart people doing that even the targeted approach would he could recruit patients. After moving to very good work on the molecular genetics prove fruitful. “The leading textbook on Yale in 1993, he and his colleagues began of cancer, cholesterol disorders and hypertension at that time made almost no studying a form of hypertension known as diabetes,” the soft-spoken HHMI investi- mention of single-gene disorders that Liddle’s syndrome, finding it to be caused gator recalls. “Yet, here was this very related to blood pressure, and there was a by mutations affecting the renal epithelial common trait, hypertension, that affects lot of skepticism that some of the diseases sodium channel. Specifically, they focused 50 million Americans and is one of the reported as single cases even existed as on a defect that allowed a flood of salt leading causes of morbidity and mortality. distinct entities,” he says. “So it was a into the bloodstream, raising blood pres- And we knew almost nothing about the pretty murky start.” sure. Another key target for study became primary determinants of this disease.” At that time, Lifton had taken a visiting the gene encoding the mineralocorticoid When he proposed to explore the genetic faculty post at the University of Utah, but receptor (MR) for the steroid hormone basis of hypertension, Lifton immediately Brigham and Women’s Hospital had also aldosterone, which regulates those sodium encountered skeptics. He remembers peo- invited him to retain his clinical position channels. ple telling him, “Hypertension is just there. This affiliation proved crucial when The first clue to MR’s key role in salt much too complicated to try to apply a colleague at the hospital, Robert Dluhy, balance came with the team’s studies of a these tools to, and you should think about encountered a patient with a rare form disease that had little apparent connection something else.” Lifton recalls that such of hypertension called glucocorticoid- with high blood pressure. David Geller, a remarks “just made me all the more con- remediable aldosteronism, or GRA. Lifton physician-scientist in Lifton’s laboratory, vinced that this was the right thing to be immediately began a genetic study of the was exploring a genetic disorder called doing.” patient and her family. pseudohypoaldosteronism type 1, which Rather than tackle the massive puzzle of “We began an investigation of this produces life-threatening loss of salt from hypertension in the entire population, he patient’s family and fairly quickly the bloodstream at birth, along with other decided to narrow his focus to genetic dis- acquired evidence that the disease was metabolic abnormalities. Geller discov- orders affecting blood pressure—choosing caused by a mutation in a particular ered that the underlying cause of this “salt just those distinctive medical puzzle pieces gene,” Lifton says. “However, the nature wasting” was a loss-of-function mutation that he could most readily fit together to of the mutation proved elusive. We finally in MR. begin building a picture of the disease. suspected that the mutation might be an The scientists reasoned that if mutations The approach echoed that of Goldstein unusual gene duplication that fused pieces causing loss of MR function produced salt and fellow Nobelist Michael Brown, who of two normal genes to create a new gene wasting, perhaps mutations that increased in the 1970s tackled the complexities of with a different function. We devised an the receptor’s activity might cause salt cholesterol metabolism by tracing the experiment to test this hypothesis. It was retention and hypertension. Sure enough, cause of familial hypercholesterolemia. one of those seminal moments—coming when Geller began to study patients with Their discovery that people with the dis- back into the lab at three in the morning early onset of severe hypertension, he

HHMI BULLETIN 25 MAY 2001 that a mutation in MR makes the that a mutation in MR makes Science In one striking discovery, Geller, Lifton Geller, In one striking discovery, laboratory have Researchers in Lifton’s Studies of the salt-regulation pathway Lifton is now zeroing in on a new blood pressure pathway. became the first to pinpoint the specific became the first to pinpoint MR, produc- mutations that overactivated ing hypertension. reported last July and colleague Paul Sigler in to proges- receptor exquisitely sensitive that this finding terone. They proposed explains why some pregnant women expe- rience dramatic spikes in blood pressure: their mutant, progesterone-sensitive MR is activated by the 100-fold progesterone increase that occurs during pregnancy. Geller is now probing the molecular details of this mutation and scouting the possi- bility that mutations in other “nuclear receptors” resembling MR might cause entirely different metabolic disorders. Such mutations might affect the receptors for hormones, such as glucocorticoid, andro- gen and progesterone itself. also pinpointed mutations that lower blood pressure by impairing salt reabsorption in the kidneys. They have shown, for exam- and ple, that diseases known as Gitelman’s syndromes, which feature low salt Bartter’s retention and low blood pressure, can arise from mutations in any of four genes. These include genes that encode cotransporters that mediate reabsorption of sodium and chloride ions, as well as genes that encode specific potassium and chloride ion chan- nels involved in this same process. by Lifton and his colleagues have revealed mutations in four genes that raise blood pressure and in eight that lower it. That body of work has unequivocally estab- lished the genetic contribution to hyper- tension, says Oliver Smithies, an Excellence Professor in Pathology and Laboratory Medicine at the University of North Carolina at Chapel Hill and a lead- Lifton’s “Dr. ing hypertension researcher. research papers are a joy to read,” says Smithies. “They go right to the heart of the problems he investigates.”

HAROLD SHAPIRO HHMI BULLETIN 2001 MAY 26 While pursuing the genet- In another promising foray, Lifton has launched studies of how BEYOND ics of blood pressure pH and magnesium levels are controlled in the kidneys.“Our Hypertension regulation, Rick Lifton has work on magnesium has taken us in some unexpected direc- encouraged scientists in tions,” he says.“We’ve ended up discovering that mutations in a his laboratory to follow their interests in other disorders whose particular class of molecules called the claudins mediate the flux secrets might yield to genetic exploration. of electrolytes through a novel pathway called the paracellular Kidney malfunction—end-stage renal disease, in particular—is pathway.” The surprise, says Lifton, is that this pathway consists of a major problem that some team members are beginning to selective pores in the tight junctions between cells that allow tackle.“If you take a broad view of big public-health problems,” certain ions to pass between the cells but not through the cell Lifton says,“in the last 30 years we’ve made substantial strides membrane.“These aren’t simple holes in the gaskets; they’re in preventing stroke by treating hypertension, and a lot of highly selective and specific pores,” he explains. progress in lowering the incidence of heart attack by reducing Working in Lifton’s laboratory on a study of families with a smoking and cholesterol levels. And yet, the incidence of end- rare magnesium-wasting disorder,Yin Lu, a physician-scientist, and stage renal disease has continued to go up, doubling every 10 Keith Choate, an M.D., Ph.D. student, have pinpointed a culprit years. So, we’ve been looking around for genetic approaches to gene named paracellin-1.This gene mediates the selective flux of end-stage renal disease, one of the most interesting of which magnesium across the tight junctions of a specific segment of the has been the most common form of glomerulonephritis, called kidney’s epithelium.The implication is that other members of the IgA nephropathy.” claudin family mediate the selective flux of ions, nutrients and IgA nephropathy affects up to 1 percent of the population even cells across body membranes. worldwide and 100,000 people in the United States alone. In other genetic studies, lab member Murat Gunel, an assistant It first shows up as blood in the urine, progressing to kidney- professor of neurosurgery, is focusing on a common neurologi- clogging deposits of the immune-related protein immunoglobulin, cal disorder called cavernous malformations, in which blood or IgA. Many patients develop kidney failure and need dialysis vessels in the brain become abnormally enlarged, causing seizures or a transplant to survive. and paralysis. He is identifying genes whose mutations can cause A number of scientists have assumed that IgA nephropathy the disease and exploring the underlying molecular mechanisms. sprang from multiple factors. But when physician Ali Gharavi, a “All these studies represent our efforts to create an environ- fellow in Lifton’s lab, studied the disease in 30 U.S. and Italian ment where young physician-scientists and postdocs can come families, he found, surprisingly, that the disease in most of the and learn human genetics and laboratory methods and then pur- families was attributable to a single genetic locus on chromo- sue problems on their own,” says Lifton.“While we certainly some 6. Gharavi reported the results in the November 2000 remain absolutely committed to our core studies of hyperten- Nature Genetics.“This falls into the category of a disease about sion, we also believe it important to explore promising new which we know almost nothing of its fundamental pathophysi- directions.The limitation, of course, is how many we can actually ology,” Lifton says.“This finding demonstrates that genetic juggle simultaneously.” approaches to this disease will likely reveal its underlying —DM biological mechanisms.”

Lifton’s group is now zeroing in on an know the genes involved and the clinical says, “is just learning something new— entirely new pathway that regulates consequences of the mutations. However, figuring out the way nature has been blood pressure. Lifton says that he and we have none of the lines to connect one working for millions or billions of years, his colleagues “have just started to crack to the other. It’s like a skier seeing, after a the way a particular human disease has one of the last remaining single-gene fresh snowfall, nothing but virgin powder worked ever since people have been on the forms of hypertension.” This pathway as far as the eye can see.” planet. Those rare moments of crystalliza- “looks like it’s going to be more interest- Clearly, Lifton still delights in scientific tion where you suddenly see into the ing than any of the others,” he says. “It’s exploration. “What I find immensely problem—those are priceless. Those are almost impossibly exciting because we exciting and satisfying about science,” he the moments that drive you.”

HHMI BULLETIN 27 MAY 2001 Overcoming the Intractable Problem

or many years, colleges and universities across the United F States have sought to increase the numbers of African American, Hispanic and Native American students who pursue scientific careers. Yet the College Board reported in 1999 that underrepresen- tation of minority students had become even “more intractable.”*

African Americans now constitute 12 undergraduates for advanced scientific percent of the U.S. population yet earned training have had uneven results. Some only 1 percent of the doctorates in 1997. have been unclear about whether their Hispanics make up 11 percent of the pop- goal is to produce scientists or just to help ulation but earned 0.9 percent of the 1997 minority students graduate. Others have doctorates. Although the numbers of been inadequately funded or lacked insti- African American and Hispanic students tutional commitment; many have never earning bachelor’s degrees in 1996–1997 been evaluated rigorously. hit an all-time high, there was a decline Some programs do succeed in helping PHOTOS COURTESY OF HAMPTON UNIVERSITY in those entering graduate school, accord- minority students graduate and pursue ing to the American Association for scientific careers. Examples include pro- the Advancement of Science. Native grams at Xavier University of Louisiana, Americans also remain underrepresented the University of California, Berkeley, and in the sciences. the University of Maryland, Baltimore Despite the best of intentions, many County (UMBC). Although different in programs designed to prepare minority important respects, these programs share

by renee twombly Increasing the Numbers of Underrepresented Minorities in Science

key features, such as clearly articulated great students and helping them succeed.” program. Today, after Villarejo took a objectives, strong institutional commit- At large universities such as UC Berkeley, chance on Willis, he is a Ph.D. candidate ment, effective mentors and an emphasis even well-qualified minority students may studying protein regulation at the on building community among partici- lose their confidence amid impersonal University of Washington. His goal is to pants. introductory courses in crowded lecture teach at a small college where he can men- All are being carried out in a legal envi- rooms during their first and second years. tor students. “Minority students fall ronment that has become increasingly “The best thing we can do,” says through the cracks all the time, and pro- complex. The University of California, for Goodman, a neuroscientist and HHMI fessors don’t often look at them and say, example, now operates under a state law investigator, “is to give these students ‘You might need an opportunity,’” Willis that forbids using state funds for special mentoring and professional advice to help says. “That can make all the difference in programs for minority students. In other them see where they are headed and then the world.” states, court cases have led colleges and offer them an environment in which they Increasing the numbers of underrepre- universities to redesign or even drop such can identify themselves as biologists.” sented minorities in science is a programs. HHMI has assisted thousands Programs such as UC Berkeley’s and “seemingly intractable task”—but it can of minority students through its under- UMBC’s are models for others to “learn be accomplished, says Peter MacLeish, graduate biological sciences education from and promulgate,” Cota-Robles chairman of the Department of Anatomy program by awarding more than $476 suggests. Campuses differ in their goals, and Neurobiology and director of the million to 232 colleges and universities. In however, such as whether to focus on the Neuroscience Institute at Morehouse 1998, it began requiring its grantees to minority students most likely to succeed, School of Medicine. The “necessary pre- certify that they are complying with all even if they come disproportionately from cursors to any solution,” he says, are relevant laws in the conduct of these pro- affluent families, or to reach out to a “sound academic advice, rewarding grams. broader group that includes students extracurricular experiences and solid Eugene Cota-Robles, cochair of the task whose paths may be rockier. foundations in mathematics, reasoning force that commissioned the College Jacob Varkey, who heads a program at and writing.” Board report, says colleges and universi- Humboldt State University in Arcata, On the following pages, the Bulletin ties must do more to help minority California, argues for the latter strategy. examines what three universities—in students become scientific leaders. “Up to “There are talented individuals who, Alabama, California and Maryland—are now, everyone working on the pipeline because of circumstances beyond their doing to help minority undergraduates approach has been thinking that bringing control, have never had a chance to show- succeed and profiles a Chicago program more students into college would solve the case their abilities,” he argues. “Everyone that seeks to interest inner-city students in problem,” he says. Cota-Robles, a profes- should have an opportunity to realize science long before they even finish high sor emeritus of biology at the University their potential.” school. of California, Santa Cruz, calls for more Merna Villarejo, who runs a program at effort to help minority students move the University of California, Davis, agrees, * Priming the Pump: Strategies for beyond the bachelor’s degree. saying that a more inclusive approach Increasing the Achievement of Under- Corey Goodman, codirector of the opens the door for students such as represented Minority Undergraduates Biology Scholars Program at UC Berkeley, Brandon Willis, whose weak math skills (New York: College Board Publications, says the emphasis should be on “taking initially barred him from the UC Davis December 1999).

HHMI BULLETIN 29 MAY 2001 NUTURING FOR SCIENCE at Tuskegee University

akeecha Tenale Reed’s professors ney disorders that are more prevalent Morehouse College, all of which, like Mcall out as they see her sniffle her among African American children. Tuskegee, have received HHMI grants. way down the hall, her voice cracking Latasha Sellers, a student from Graduates of these schools are much from a bad cold. “Makeecha! Are you Georgia, also hopes to become a physi- more likely to pursue M.D. rather than better today?” asks geneticist John cian—in her case, to provide primary Ph.D. degrees; since 1996, only seven Williams, who also inquires about her care to an underserved community. As Tuskegee students have entered graduate medical school applications. Biology pro- she entered her final semester at school in the life sciences. Stephen fessor Velma Richardson drapes her arm Tuskegee, she was preparing for several Nurse-Findlay, 29, who graduated from around the young woman, and James medical school interviews. Tuskegee in 1995 with degrees in both H.M. Henderson—Tuskegee’s 83-year- The small Alabama campus illustrates biology and chemistry, is among those old statesman of science education— both the importance and limitations of who became physicians. A recent gradu- teases her about being named Miss the nation’s historically black colleges ate of an M.D., M.P.H. program at The Tuskegee University. Then he asks about and universities, which produce a dispro- Johns Hopkins University, he looks back her latest lab assignment. portionate number of African American and says that Tuskegee’s primary appeal Reed, a 21-year-old from North students who apply to medical school. was “the feeling of being very supported Carolina who has a 3.9 grade-point aver- The Association of American Medical and nurtured. If you want to accomplish age, came to this historically black uni- Colleges (AAMC) notes that 18 Tuskegee something, the people at Tuskegee are versity for just such support. “Professors students applied to medical schools in going to help you. I loved it.” know me, and I feel appreciated,” she 1999 and eight were accepted. Xavier Another Tuskegee alumnus, Emmitt says. “They drive me hard and they chal- University of Louisiana topped the Jolly, took the other path and will soon lenge me constantly.” Reed hopes to AAMC’s list, followed by Howard receive a doctorate in biochemistry at the become a pediatrician specializing in kid- University, Spelman College and University of California, San Francisco.

NATIVE AMERICAN STUDENTS Straddling Two Worlds

n the living room of a bungalow on society and the other in the larger world. research opportunities and introduces I the Humboldt State University campus Indian culture stresses cooperation rather them to role models such as Boham, a in northern California, Rachel Mayfield, than competition, Boham points out, and Little Shell–Chippewa Indian, and mem- a Cherokee Indian who hopes to earn some tribes proscribe practices such as bers of organizations such as the Society both an M.D. and a Ph.D., is rehearsing dissection. Family generally takes prece- for the Advancement of Chicanos and a medical school entrance interview. “If dence over school or career, poverty is Native Americans in Science (www.sac- they ask if my medical education comes common, and both educational resources nas.org) and the American Indian Science before everything else in my life, I’m and role models are limited. and Engineering Society (www.aises.org). going to have to say no,” she declares. “We want to help students develop the Then there’s the program house, which “Medical school is very important to me, traits that will enable them to succeed in Mayfield calls her home away from but if someone in my family needs me, the dominant society and at the same home. Although they don’t live there, I’m on my way home. Family comes time strengthen their connection with students have access 24 hours a day and first.” their tribal culture,” Boham explains. band together there. “We all have attacks “Rachel,” says Russell Boham gently, “We’re not taking anything away from of self-doubt,” says Mayfield, who has a “we need to talk.” them. We’re giving them additional tools, 3.8 grade-point average with a major in Boham, who sports long black braids so they can walk in both worlds.” cellular and molecular biology and and has a bachelor’s degree in biology To do that, the program provides stu- minors in applied mathematics and and a Ph.D. in adult education, heads a dents with academic assistance, career Native American studies. “When I feel program at Humboldt State that helps advice and personal counseling, which like I don’t belong in college and couldn’t Native American students succeed in the helped keep Mayfield on track while possibly go to medical school or gradu- sciences. His goal, he says, is to help stu- weathering family problems. The pro- ate school, someone who is feeling more dents walk with one foot in their tribal gram also helps students find summer confident that day helps me through it.

HHMI BULLETIN 30 M A Y 2 0 0 1 Makeecha Tenale Reed can count on encouragement and academic challenge from professor emeritus James H.M. Henderson and other faculty members at Tuskegee.

Jolly, the 26-year-old son of a rural promising African American students go istry and related fields. Henderson con- Alabama locksmith, is now deep in the to state schools such as Auburn or the curs, arguing that success in science THOMAS MARTINTHOMAS hunt for a transcription factor that con- University of Alabama, which have both depends more on a student’s attitude and trols meiosis. He says Tuskegee offered lower tuition and environments quite confidence than on high-tech equipment. limited opportunities on campus to different from that at Tuskegee. When it comes to producing successful carry out cutting-edge research but pro- In the late 1980s, Henderson applied science graduates, Nurse-Findlay sug- vided “a firm grasp of who I was and successfully for an HHMI grant, subse- gests that historically black colleges and personal support that pushed me to go quently renewed three times for a total universities like Tuskegee can hold their to the next level.” of $2.7 million, that has enabled own against larger, better-funded pre- Still at Tuskegee, Sellers adds that Tuskegee to provide an eight-week sum- dominantly white institutions because of “biology is biology, whether here or at mer program for entering students inter- the high level of emotional comfort they Harvard. What you get here are small ested in science. The program helps the are able to provide. “While funding is classes and faculty that know your students not only prepare for science clearly important, I believe that intellec- name and work with you one on one. classes but also improve their computer tual challenge combined with consistent- The faculty want you to achieve here, and reading skills. Many of these ly positive reinforcement from faculty is and they expect you to.” “bridge program” participants spend a more accurate predictor of success in This emphasis on personal attention subsequent summers doing research at science and medicine,” he says. offsets some of the problems that a top-notch universities and research insti- Like many colleges and universities school like Tuskegee faces in attracting tutions across the country, an experience across the country—large and small, top high school students. As a small pri- that leads more than half of them to public and private—Tuskegee has found vate university established in what was enter professional health fields or pursue that nurturing and mentoring are essen- then an officially segregated society, it advanced degrees in science or medicine. tial to helping minority students pursue still lacks many resources. “Success in “We don’t propose to be a research- scientific careers successfully. Like every attracting the best students revolves intensive university, but students are campus, it also has incorporated those around money,” says Henderson, a more than prepared when they leave ingredients into a unique recipe that fits Howard University–trained plant physi- here,” says Richardson, who notes that its own niche and goals. ologist whose office is blanketed with Tuskegee recently established a laborato- Renee Twombly photographs of present and former stu- ry facility where students can carry out dents. Even within Alabama, many research in molecular biology, biochem-

Then I do it for someone else who is Although small, Humboldt State’s pro- down when I am up.” gram seems to be having an impact,

Mayfield grew up in a rural area in attracting the highest percentage of WALKER SHAWN northern California, both on and off Indian students in the California State reservations. She finished high school University system. During the past three and went to work. “I didn’t know any- years, 10 Native Americans have one who had gone to college, so I never majored in life sciences at Humboldt even thought about it,” she recalls. Lured State. Of the four who were chosen to back into school by a friend’s physics conduct research in the HHMI program, teacher at Mendocino Community one is now in medical school, another is College, she met Boham at a Native in graduate school, a third is applying to American day there and braved a visit to medical school, and the fourth is Humboldt State. “For the first time I Mayfield. Last year, the university was thought, ‘I could do this,’ ” she says. She recognized nationally with one of 10 now works in the lab of her adviser, biol- Presidential Awards for Excellence in ogy professor Jacob Varkey, who heads Science, Mathematics and Engineering an HHMI-supported undergraduate bio- Mentoring. logical sciences education program on “These are talented students,” says the campus. She hopes to practice medi- Humboldt State President Alistair cine and do genetics research on Native McCrone. “Our role is to catalyze and Rachel Mayfield (left) and Laurel American health issues, such as the high release those talents.” Prince practice playing a traditional rates of diabetes and breast cancer. Jennifer Boeth Donovan Native American drum. UMBC’s Formula for Success

hat specifically can a university do potential students to the campus for a W to boost the number of minority weekend to visit with faculty, staff and students who will go on to pursue gradu- current undergraduates. ate studies in science? n Providing entering freshmen with a The University of Maryland, Baltimore summer “bridge” program that includes County (UMBC), offers answers. Recent math, science and humanities course- studies point to a remarkable record of work; training in analytic problem success at this public research university. solving; opportunities for group study; Much of the success focuses on the uni- and social and cultural events. versity’s Meyerhoff Scholars Program, n Offering comprehensive merit scholar- which attracts promising minority stu- ship support and making continued dents to the predominantly white school. support contingent on maintaining a B Participants in the program, which began average in a science or engineering in 1988, are nearly twice as likely to major. graduate in a science, engineering or n Fostering active faculty participation in mathematics discipline as peers who recruiting, teaching and mentoring. decline admission to the program and n Emphasizing the importance of out- enroll elsewhere. Since 1993, 234 standing academic achievement, partici- Meyerhoff scholars have earned degrees pation in study groups, collaboration in these disciplines, with 85 percent going with faculty and preparation for gradu- on to graduate and professional programs ate or professional school. nationwide. n Involving the students in sustained, sub- The students work part time in labora- stantive research experiences during tories during the school year and full time both the school year and the summer. during the summer. These sustained n Encouraging the students to use depart- PAULFETTERS research experiences lead to close ties mental and university tutoring with faculty mentors and, often, to publi- resources, with an emphasis on high cation of scientific papers. Freeman A. academic achievement. Hrabowski III, UMBC’s president, and n Maintaining strong support by the uni- Michael F. Summers (left) and Freeman Michael F. Summers, an HHMI investiga- versity’s administration. A. Hrabowski III both serve as tor and professor at the university, tell the n Providing academic advising and per- mentors for UMBC students. Bulletin that the program succeeds sonal counseling. “because the faculty and administration n Linking the students with mentors from are committed to making the production professional and academic fields in sci- The Meyerhoff Scholars Program of minority scientists a major priority.” ence, engineering and health. They also maintain that “with a similar n Encouraging a strong sense of commu- nity among the students. succeeds "because the faculty and commitment, other universities can repli- cate many of the program’s best practices n Involving the students’ parents and and help to produce many more minority other relatives who can be supportive. administration are committed to graduates in science, engineering and n Soliciting public and private financial mathematics across the country.” support. making the production of minority Hrabowski and Summers say the fol- lowing components are critical to the The program also encourages students scientists a major priority." success of the program, which is described to talk with a variety of scientists, on and online at www.umbc.edu/Programs/ off campus, about research in order to Meyerhoff/Undergrad: gain as much information as possible to help in making decisions about their own n Recruiting top minority students in research interests and career paths. math and science, in part by bringing

HHMI BULLETIN 32 M A Y 2 0 0 1 ROBB ROBB HILL

HOOK THEM YOUNG Hold Them in Science

Program coordinator Morgan Scholten (left) and intern DeAngelo Jones show Girl Scouts a box turtle that is native to the Chicago area.

y 2020, Memory Cain may be a sur- students with a one-time auditorium-style graduates are in college or planning to go, Bgeon. Then again, she may not. “It’s a program. “We chose to try a different many with hopes of pursuing careers in lot of school,” says the 16-year-old high approach,” explains Jennifer Blitz, the science and medicine. Otilia Pineda, who school junior from the gritty streets just academy’s vice president of education and participated in 1996, will complete a bach- west of downtown Chicago. “But that’s HHMI program director. “We wanted to elor’s degree in biology and psychology at what I want to do.” see if intensive attention could make a big DePaul University this spring and plans to Colleges and universities, which often difference in a small number of lives.” go to graduate school. Eduardo Roman, a compete with one another to attract the Recognizing that academic grades do not high school senior, hopes for a career in most talented minority students, need necessarily predict scientific performance, biochemistry. All the participants, regard- more teenagers like Cain to help expand particularly at a young age, Blitz’s staff less of their plans, have learned more the pool of qualified applicants. The decided to target average students who about science. Chicago Academy of Sciences is trying to express an interest in science. Some of the Program coordinator Morgan Scholten make sure that she and others are truly teenagers have barely a C grade-point has advice for other institutions that might prepared. With HHMI support, the acade- average, says Melanie Napoleon, the develop similar programs to help prepare my brings Cain and 15 other sophomores museum’s manager of enrichment pro- more minority teenagers to pursue careers and juniors from Chicago public high grams. “We take kids at different stages in in science and medicine. “Involve teachers schools to its Peggy Notebaert Nature their development,” she explains, “and we and families from the beginning and keep Museum on Saturdays to work with scien- expose them to each other and to as much them informed; they are essential in tists and talk about career opportunities. science and as many scientists as possible, recruiting participants and keeping them in The teenagers also serve as museum volun- because you never know which seed will the program,” she says. “You also need to teers, learning science as they explain it to take root and grow.” help the teens get to know each other, and younger children and their families. The program, which includes children of put them at ease with games and other The program focuses on mentoring at recent immigrants, is a labor-intensive, group activities. And give the youngsters every level, with museum staff guiding the high-maintenance effort, supported since real work to do, even if it is not directly teenagers, who in turn teach younger 1993 by two HHMI grants totaling related to science. Being entrusted with children such as Girl Scouts working on $450,000. Just over 100 youngsters have independent tasks helps teens develop self- science badges. For the same price, the completed it. Is it worth the price? “We confidence.” museum could have reached hundreds of think it is,” says Blitz. Most of its Jennifer Boeth Donovan

HHMI BULLETIN 33 M A Y 2 0 0 1 FROM THE TOOLBOX

Dam! A New Method for m Pinpointing Gene Transcription

In February, the human genome was pub- member of the Fred Hutchinson Cancer lished in science journals, the result of Research Center in Seattle, has a long- the labor of a multitude of scientists standing interest in gene function and the around the world. Now researchers face structure of chromatin, the mass of pro- the daunting task of explaining how teins surrounding chromosomes that human genes turn on to produce the pro- plays a role not only in transcription but teins they encode. What activates T cells also in such functions as cell division and in the immune system, for example, to DNA synthesis. He and van Steensel set respond to an infection? How do cells in out to track the destinations of these the womb know they must grow and mysterious proteins, which meant using divide to form an eye or an arm or a set living cells and ruled out the use of chro- of nerve cells? matin immunoprecipitation because of its The answer lies with transcription fac- toxic effects. tors, which account for as much as 10 The two scientists pondered possible DamID percent of the genome in humans and alternatives. They needed a signal of other organisms. Transcription factors, some kind to show them where each pro- which are themselves proteins, travel to a tein was binding to its target on the cell’s nucleus to turn genes on, telling DNA. So, they fused the proteins to a

them to start producing their particular chemical signal: an enzyme called ade- NEWMAN KELCEY proteins. Or, they may turn genes off. nine DNA methyltransferase, known as Either way, they send their message by Dam. m binding to the end of a gene and recruit- In the method they developed, each ing the cell’s machinery to spur the gene protein, accompanied by Dam, is sent into action. into a genome to find its matching DNA A transcription factor consisting of mul- Despite their large numbers and critical sequence. In the case of transcription fac- tiple protein subunits, shown here as role, transcription factors remain poorly tors, the protein latches on to its target colored balls, binds to its DNA target. understood. The newly published gene, thereby sending the signal to begin One of the protein subunits is fused to genome, in other words, is like an the transcription process. The protein’s Dam (the yellow ball connected by a instruction manual describing thousands traveling partner, Dam, also grabs hold green linker segment). This tethered of parts that no one is quite sure how to of the DNA and attaches a group of Dam grabs hold of each nearby “recog- spur into action. In large part, that’s chemicals called methyls to the DNA nition site”—the DNA sequence shown because researchers lack an effective flanking the gene. The scientists then cut as GATC—and attaches a methyl method for matching up transcription up and remove the DNA near the methyl chemical group (m) to it. factors with their “gene targets.” The groups, and these fragments reveal the most widely used method, called chro- sequence of the DNA that matches the matin immunoprecipitation, is toxic to protein. “gene chips”—microarrays that contain cells and often ineffective. Dubbed the DamID method, this new numerous DNA sequences—and tiny col- Bas van Steensel, a former postdoctoral tool, which should accelerate the study of ored labels that glow when genes are fellow with HHMI investigator Steve transcription factors, at first could be activated. Now, they’re able to isolate Henikoff and now the head of a lab at used only to examine a single target at a not one but many sections of DNA that the University of Amsterdam, came up time. That was a problem because, as match up with a transcription factor and with a better approach. He and Henikoff Henikoff points out, a single transcrip- to deduce where the sections are located collaborated to develop a technique that tion factor may actually “bind to dozens on the helix. may enable research on transcription fac- or hundreds of targets throughout the Other researchers have also begun tors to make significant progress. genome.” using microarrays to study gene expres- At the time, they weren’t even thinking He and van Steensel went on to make sion patterns, but this new method about transcription factors. Henikoff, a the method more useful by incorporating allows one to “see where transcription

HHMI BULLETIN 34 APRIL 2001 factors actually bind, which may be an NEWS & NOTES important prerequisite for gene expres- sion,” Henikoff says. “In many cases, this mice that were normal in every way approach will give you a more direct Fine-Tuning a except that their BK channels lacked a readout of gene regulation. People have single component, called the β1 subunit. talked about using microarray analysis to Blood Pressure This modification rendered the channels study genes that are coexpressed, but we less responsive to calcium release, and can do it with the transcription factors Regulator the mice developed high blood pressure themselves and look at where they’re and other abnormalities caused by binding genes to activate or silence them. In a study in mice, researchers have chronic hypertension. I think that’s the major value of this found evidence that high blood pressure The physiological effects were so approach.” may be controllable by drugs that target straightforward that the β1 subunit The approach is attracting notice. a particular type of ion channel found in appears to be a promising target for “The paper by van Steensel and Henikoff the smooth muscle cells surrounding new antihypertension drugs. “Drugs describing a method that allows one to arteries. The drugs would specifically that change β1 subunit function by find needles in a haystack made me get affect the release of potassium ions, altering the channel’s calcium sensitivity up from my desk and rush to the labora- which play important roles in regulating could allow control of blood pressure tory,” says transcription expert Danny blood pressure. up or down with fewer side effects than Reinberg, an HHMI investigator at the The research team, led by HHMI current treatments,” Aldrich says. University of Medicine and Dentistry of investigator Richard W. Aldrich at Having these mice available may also New Jersey. “It’s allowed us to see the Stanford University, focused on the so- help advance basic research in hyperten- light at the end of the tunnel as we called BK channels. When a burst of sion. Says Aldrich, “Since we can alter attempt to define one or more genes that calcium is released from intracellular this subunit to affect blood pressure are recognized by a protein whose expres- sites within smooth muscle cells, the BK without affecting other systems, we can sion causes cells to stop dividing. I predict channels in those cells open, potassium use it as a model to study hypertension this technology will be used worldwide.” ions flood out, the smooth muscle re- beginning at the molecular level, In addition to spurring basic research, laxes and blood pressure goes down. through cellular physiology, to the Henikoff and van Steensel’s technique Calcium entering through the surface pathology and long-term ramifications might be used for diagnostic purposes. membrane, however, can also cause of the disorder.” For example, some researchers are now blood vessels to constrict, causing high In addition, the study indicates that using microarray analysis to correlate blood pressure. the gene controlling production of the patterns of gene expression with different “Thus, there’s a balance involved in β1 subunit may be involved in inherited types of tumors and with how these types regulating blood pressure,” Aldrich says, forms of hypertension, some of which respond to various treatments. “The “and we are hoping to learn how the BK have not been pinpointed to specific DamID method can provide the same channel acts to tip that balance toward genes. “These findings suggest that this information,” Henikoff says. “But where dilation.” is a good candidate to examine to see if microanalysis provides only a single read- In their study, reported in Nature, the humans with hypertension have muta- out regarding the expression pattern of researchers created genetically modified tions in this gene,” Aldrich says. H genes, DamID may be able to provide a different readout for each transcription “Since we can alter factor that affects a single type of cancer cell. Thus, the method has the potential this subunit to to greatly increase the power of cancer profiling.” affect blood pressure Indeed, good things may result as scien- tists identify the binding sites for proteins without affecting other encoded by the oncogenes and tumor- suppressor genes that loom so large in systems, we can use it cancer. “For example,” says Henikoff, as a model to study “the myc oncogene, which is being stud- ied by my Hutchinson colleague Robert hypertension Eisenman, encodes a transcription factor that has unknown targets. If our new beginning at the method proves useful in determining the RIES BARBARA gene targets for myc, then this knowledge molecular level.” may help elucidate how misexpression of —Richard W.Aldrich myc causes cancer.” Jim Kling HHMI BULLETIN 35 APRIL 2001 NEWS & NOTES Medicine and Computing Converge in a New Career

Atul Butte’s career boils down to one relationships between genes and anti- Butte graduated from Brown word: convergence. For years, his inter- cancer drugs. They found that low levels University, where he participated in a ests in medicine and computer science of the protein LCP1, which is produced program for students who want to pur- remained separate. Then the Human by a gene implicated in several forms of sue undergraduate studies and medical Genome Project took off just as Butte cancer, predicted the susceptibility of the school at the same time. He first earned a was finishing his medical training, and he cancer to the drugs. bachelor’s degree in computer science, found himself in the vanguard of the hot Now, the researchers are using the and then an M.D. In 1993, just before new field of computational biology. technique to identify the gene interac- his fourth year of medical school, he Today, Butte is developing genomic tions that lead to diabetes. “If we find stepped away from his formal course- techniques to study such complex dis- the genes that are responsible, then we work to spend a year at the National eases as type 2 diabetes mellitus. can screen children to know which ones Institutes of Health (NIH). Working Working at Children’s Hospital in need to lose weight to avoid getting dia- through the HHMI-NIH Research Boston, he is a clinical fellow in pedi- betes in adolescence,” Butte says. “We Scholars Program, Butte carried out atrics and a fellow in endocrinology and can also help find targets for new drugs research on signal transduction involving informatics. “Although I am specializing for diabetes.” insulin receptors. in diabetes genomics,” he says, “I am Companies specializing in biotechnolo- After returning to Brown and receiving developing algorithms and tools along gy have tried to lure him from academia, his medical degree, Butte moved to the way that will assist many others who but Butte says he prefers to stay at an Children’s Hospital for his pediatrics are doing research with functional academic hospital, working in the pedi- residency and fellowship. In 1998, his genomics, whether or not they are in the atric diabetes clinic and juggling a variety adviser introduced him to microarrays, diabetes field.” of projects involving functional genomics. the new microscopic “gene chips” that One such tool, created in 1999 by Now that his dual career paths have simultaneously reveal the activity of tens Butte and his adviser, Isaac Kohane, is intersected, he says he wants to enjoy the of thousands of genes. Microarrays yield the “relevance network for genomic data view. As he describes the convergence, mountains of data that must be analyzed mining,” which can analyze large Butte frequently launches into spirited to determine the patterns by which the amounts of data about RNA expression discourses on issues such as medical edu- profiled genes switch on and off—infor- in cells and identify important interac- cation and intellectual property rights. mation that gives researchers new insight tions between genes. Last fall, in the He becomes particularly animated as he into why a disease occurs and how it Proceedings of the National Academy of recounts the events of the past two years, might be stopped. Butte’s relevance- Sciences, Butte and his colleagues re- when his parallel interests finally began network technique helps make sense of ported using the technique to uncover to merge. such data. “If you look at my CV, it looks like I planned my career,” he says. “But it was simply a matter of taking advantage of “I am developing being at the right place at the right time.” This past September, recognizing algorithms and tools that the “right place” is an ever-moving target, Butte entered a doctoral program along the way that will in health sciences technology at the Massachusetts Institute of Technology, assist many others who where he’ll specialize in medical engineer- ing and medical physics. He also spends are doing research with considerable time on the road, speaking at academic institutions and consulting functional genomics, or giving presentations on computational biology and related topics at companies whether or not they are involved in medical informatics. H in the diabetes field.” Delia K. Cabe —Atul Butte TNE ROWIN STANLEY How Sperm Jump-Starts the Embryo When it comes to sexual reproduction, eggs are relatively easy to extract, have just say NO. That’s because nitric oxide long served as a model for fertilization (NO) appears to jump-start the process studies. Epel and others discovered the

by which a sperm and an egg form an vital role that calcium plays in activating TEGNER OF MIA COURTESY embryo, at least in sea urchins. Richard all eggs, including those of humans, in Kuo, who was an HHMI predoctoral fel- experiments on sea urchins during the low in the Stanford University laboratory 1970s. If nitric oxide turns out to play a of David Epel, recently discovered the role in mammalian fertilization similar to mechanism that has puzzled biologists that in sea urchins, then new treatments for decades. In an article in Nature, Kuo might become possible for certain forms and colleagues reported that NO gas of male infertility. builds up inside the sperm of sea urchins. The Stanford team has created an A scanning electron microscope shows a When a sperm attaches itself to an egg, animation of the process. It is available single sea urchin egg surrounded by the sperm injects its load of NO, online at www.stanford.edu/group/ thousands of sperm. Fertilization occurs triggering the release of calcium and Urchin/nos.htm as part of a larger when one sperm attaches itself to the egg thereby sparking the development of an educational site on sea urchin and injects nitric oxide gas. The image is embryo. Sea urchins, whose sperm and embryology. H magnified nearly 3,000 times.

Former HHMI predoctoral fellow Richard Kuo (center) David Epel (right) and research team member Chris Patton (left) use Pacific sea urchins to unravel the mysteries of fertilization in animals. JACK HUBBARD JACK HUBBARD

Biologists extract sperm and eggs from sea urchins, the small, spiny, purple invertebrates that are widely used in fertility research.

HHMI BULLETIN 37 APRIL 2001 NEWS & NOTES

school system’s new superintendent, Paul ‘First Light’ Gives D.C. Students a Vance. “Now there’s some accountability and some understanding of what stan- Second Chance to Discover Science dards are,” Cifuentes says. “The academic achievement data for the D.C. In the Carnegie Institution of Washington’s That effort in turn led Carnegie to join public schools show starkly how few stately marble halls, a few blocks from with the D.C. school system and the students will have the opportunity to the White House, 30 students from the American Association for the succeed if the status quo is maintained. city’s elementary schools are learning to Advancement of Science in a program to School staffs are now examining that test think like scientists. improve science and math instruction at data and looking for ways to improve “Here’s what good scientists do,” says 21 of the city’s elementary, middle and instruction. The Carnegie Academy for teacher Greg Taylor. “They ask lots and high schools. HHMI contributed an Science Education is working with them lots of questions.” Dominic Gasaway, 12, additional $450,000 grant to provide in 15 elementary schools.” promptly responds by asking how the stereoscopes, magnets and other tools for This kind of partnership between an water, salt and flour that he is mixing in the new effort, called DC ACTS. urban school system and private scien- a big green bowl will result in a sub- Carnegie launched the program for tific organizations can make a real stance resembling Play-Doh. Can the teachers at a difficult time for the school difference, according to Bob Rice, vice mixture be cooked? Will extra flour system, which was grappling with fre- president of the independent D.C.-based make the goo stretch farther? Will it quent changes in superintendents, Council for Basic Education. Such efforts smell like the store-bought stuff? disputes on the school board, dismal “let students reach beyond what they get Thus begins another day of discovery student test scores and low graduation in school and capitalize on their inter- at First Light, a five-hour “science rates. “When we tried to approach the ests,” he says. “They also give those school” offered every Saturday by the school system, there was just no inter- students who may be somewhat reluctant Carnegie Institution, with HHMI sup- est,” says Ines Cifuentes, who directs the in the classroom another chance to port. Named for the illumination that effort. Eventually, however, by spending investigate science in a totally different fills a telescope when its lens is opened, time in the schools with principals and atmosphere.” First Light has been turning Saturdays teachers, she and her colleagues estab- Young Dominic seems to be benefiting. into science days for D.C. schoolchildren lished an effective relationship. As Soft-spoken and shy, he discovered the since 1989. The class gives inner-city stu- evidence of the program’s success, an First Light lab when he was five years dents in grades three through six a independent assessment has shown that old, tagging along behind his older chance to experience the excitement of many of the teachers “lost their fear of brother, Edwin. Now, he aspires to science—and it is thought to boost their science and came to appreciate that become a science or math teacher. “We self-esteem in the process. science can be a powerful tool for learn interesting new stuff here all the First Light has room for 30 children motivating children to learn.” time,” he says, “and this has helped me per session—first come, first served. The By contrast, the DC ACTS program get A’s in science in school.” H program’s impact, however, reaches far has been embraced from the start by the Melody Simmons beyond its little classroom and laborato- ry. Its students have gone on to shine in science and mathematics in high school and to major in them in college. The program also inspired the Carnegie Institution—a private, nonprofit organi- zation focusing on scientific research and education—to establish an intensive, six- week summer program for local elemen- tary school teachers. Since 1994, the pro- gram has helped more than 400 teachers learn new techniques of science teaching.

Dominic Gasaway adds fine sand, course sand and gravel to a tube of water held by teacher Greg Taylor, as fellow students time how long each material takes to settle to the bottom. WILLIAM K. GEIGER

HHMI BULLETIN 38 APRIL 2001 The data came from some of the and only one said before 8 a.m. All but Teens Tend to 200 Washington, D.C.–area teens who four of the students said they’d rise by attended the annual lecture series at noon. Three preferred to sleep until 1 Be Night Owls HHMI headquarters in Chevy Chase, p.m., and one said after 2 p.m. “More Maryland. They and adult volunteers teenagers are night owls than are morn- On weekday mornings, it’s hard to tell from the Institute’s staff participated in a ing larks,” Takahashi noted. “Lots people who are natural “larks” from sleep study before the lectures, filling out more.” those who are “owls.” Data presented at questionnaires about their sleep prefer- Takahashi and Michael Rosbash, an HHMI’s Holiday Lectures on Science in ences and wearing activity-measuring HHMI investigator at Brandeis December showed that teenagers and devices on their wrists for 11 days. University, presented four lectures on cir- working adults both wake consistently Joseph S. Takahashi, an HHMI investi- cadian rhythms and their research into between 6 and 7 a.m. on weekdays, since gator at Northwestern University and the physiology and genetics of biological they have to go to school or their jobs. one of the two lecturers, highlighted the clocks. Videos of the talks and related But on weekends, working adults tend to striking findings during his first talk. “If teaching materials are now available wake up no more than an hour later than you had your choice,” he asked the audi- online at the Holiday Lectures Web site, usual, while most teens sleep until 10 ence, “when would you like to wake www.holidaylectures.org. H a.m. or later—sometimes much later. up?” Three students chose before 9 a.m. Jennifer Boeth Donovan

FRIDAY 03-NOV SATURDAY 04-NOV

00:00 06:00 12:00 18:00 00:00 00:00 06:00 12:00 18:00 00:00

16-year-old-male wakes up at 6 a.m. weekdays wakes up at noon weekends

44-year-old-female wakes up at 7:30 a.m. weekdays wakes up at 6:30 a.m. weekends

Hungary (8), Czech Republic (6), Estonia HHMI Awards (4), Poland (3), Lithuania (3), Slovakia (2), Ukraine (1) and Bulgaria (1). HHMI $15 Million to selected them in a competition on the basis of their accomplishments, creative poten- European tial and research plans. This is HHMI’s second round of Researchers grants in the region. In 1995, it awarded $15 million in HHMI has awarded new grants totaling grants to support the $15 million to 46 biomedical researchers research of 90 scien- from nine countries of the Baltics, central tists, as well as their and eastern Europe and the former Soviet students, laboratory Union. teams and institu- The scientists will each receive between tions. More infor- $225,000 and $450,000 over five years to mation about the do research in areas ranging from protein program, and a list of folding to multidrug resistance in cancer. the new grants, is available online at Among them are citizens of Russia (18), www.hhmi.org/international. H

HHMI BULLETIN 39 APRIL 2001 NEWS & NOTES Untangling the Web of Yeast Protein Interactions Cells contain large numbers of proteins, which interact with each other in myriad ways. But how do all the interactions fit together? A team of researchers led by HHMI investigator Stanley Fields at the University of Washington has provided a new view of the situation with a map showing the networks of protein interac- tions in yeast. The map is based on more than 2,700 protein interactions involving 2,039 yeast proteins. Peter Uetz, a former HHMI associate at the University of Washington, also participated in the study, which was published in the December 2000 issue of Nature Biotechnology. Although Fields and his colleagues cau- tion that the map likely contains errors and omissions, they believe it is a first step toward providing scientists with a reference guide to aid detailed explo- ration of the functions of yeast proteins. “Protein-interaction data allow you to place an uncharacterized protein in a metabolic pathway, a cellular structure or a macromolecular complex,” Fields says. “Once you have that information, you can carry out experiments to understand that protein based on those associations.” A small section of an interaction map of yeast proteins. Proteins are colored according The researchers tested the validity of to their functional roles, with proteins involved in membrane fusion (blue), lipid their interaction map by assessing how metabolism (yellow), chromatin structure (gray), cell structure (green) and cyokinesis reliably it enabled them to predict the (red). Proteins involved in the same process tend to cluster in a region of the map. functions of 1,393 previously character- Reprinted by permission from Fig. 1, Nature Biotechnology 18:1258, 2000 ized proteins. The map yielded a correct © Macmillan Magazines Ltd. prediction 72 percent of the time, Fields says. The map is an important beginning, in humans will yield more insight into protein, making such networks even but “it is clear that over the next few protein function. more useful in guiding research. years, the yeast-research community will Future versions of interaction maps “Ultimately,” he says, “one would like to produce more protein-interaction data, likely will be aided by advances in superimpose on these interaction maps and we can use that information to build computer graphics, which will enable such cellular structures as the nucleus, more complex networks,” Fields says. scientists to create displays in three cytoplasm and plasma membrane, making Likewise, efforts to map protein interac- dimensions. Fields also predicts that the maps one component of a ‘virtual cell’ tions in the roundworm C. elegans, in future maps will contain hyperlinks that that contains a variety of information the fruit fly Drosophila melanogaster and direct users to detailed data about each about its molecules and structures.” H

HHMI BULLETIN 40 APRIL 2001 While the experiments raise the possi- Vaccination Experiment Casts bility that a vaccine against Alzheimer’s disease might slow or prevent progression a Key Guilty Vote Against Amyloid of the disease in humans, St. George- Hyslop remains cautious. “While . . . this in Alzheimer’s vaccine seemed to affect the pathology of the disease and also to affect cognitive The accumulation of dense plaques of peptide is a significant player—although function, the mouse is not a perfect model beta-amyloid (βA) peptide outside brain maybe not the only player—in generating for human Alzheimer’s,” he says. “So it is cells is one of the hallmarks of Alzheimer’s Alzheimer’s disease,” St. George-Hyslop conceivable that a vaccine that works well disease. These plaques are believed to says. The study also may lay the ground- in mice may not work well in humans.” cause neuronal breakdowns, which lead work for developing a vaccine against An Alzheimer’s disease vaccine for to dementia. this devastating disorder. humans might not raise a substantially Now, scientists at the University of How the vaccine works to improve robust immune response in elderly Toronto, led by HHMI international memory is not clear, he says. The overall patients, whose immune reactivity might research scholar Peter St. George-Hyslop, level of βA peptide in the brains of the be lower, St. George-Hyslop says. The are using some of these same βA peptides mice did not fall after vaccination. Such vaccine also might provoke an auto- to vaccinate mice that have been geneti- a decline might have been expected, immune response that leads to tissue cally engineered to develop a disease sim- since previous research had shown that destruction, or it might interfere with nor- ilar to human Alzheimer’s. The vaccines cognitive ability declines as βA deposi- mal processing of amyloid proteins. appear to be having an effect. In a study tion in brain plaques increases. “However, an important implication reported in Nature, the researchers found Vaccination did, however, reduce levels of this study is that even if a vaccine turns that the vaccinated mice performed of a particular subset of βA deposits, out to be a bust, other treatments directed markedly better in memory tests than did called cerebral fibrillar βA, that might at manipulating beta-amyloid processing mice that were not vaccinated. be critical in the formation of the long are likely to be helpful in alleviating “This finding represents one more ele- fibrils that contribute to the formation Alzheimer’s disease,” St. George-Hyslop ment of the proof that beta-amyloid of plaques. says. H

In their study, reported in the Fruit Fly Gene Survey Finds Correlation December 5, 2000, issue of Proceedings of the National Academy of Sciences, Between Aging and Free Radicals the scientists found that while many of the genes exhibited changes in transcrip- tion level because of both aging and Fruit fly studies may improve our under- damage that may contribute to age-related paraquat exposure, the specific changes standing of the genetic basis of aging and deterioration of cells. The scientists then observed were often not the same in the role that chemicals called free radicals used DNA microarrays to monitor gene both groups of flies. Furthermore, the play in the aging process, according to a expression in both groups of flies to see if “coregulated” genes—those that behaved research team led by HHMI investigators similar groups of genes were activated the same in both groups—included 33 Lily Y. Jan and Yuh Nung Jan at the during normal aging and in response to percent of the age-regulated genes and University of California, San Francisco. free-radical stress. 18 percent of the paraquat-regulated In order to study gene activity during “The idea for our study arose from genes. “Based on that finding,” says Yuh “normal” aging, the researchers collected Seymour Benzer’s finding at Caltech that Nung Jan, “we think there is merit to one group of flies selected at 3, 10, 15, 25, methuselah mutant flies have longer life the free-radical idea of aging, but it also 30, 40 and 50 days of age. Only a small spans and are more resistant to oxidative is clear that it is not the whole story.” percentage of flies live past 30 days; thus, stress,” says Yuh Nung Jan. “Also, if you The scientists emphasized that their the 40- and 50-day-old flies were relatively look at the curve of the percentage of sur- study could not determine whether the ancient. viving flies as a function of age, it is quite changes observed in gene activity were a A second group, composed solely of 3- similar to the curve of surviving flies treated cause or an effect of aging. “But this day-old flies, was treated with the pesti- with paraquat. The time course is very dif- study enables us to single out candidate cide paraquat, which produces free radi- ferent, but the curves are quite similar. So genes,” Yuh Nung Jan says, and then cals in flies’ cells. Free radicals are highly there might be some general shared mecha- “do further studies to see whether the reactive atoms or groups of atoms that nism, and we might see a similar change in genes have an effect on the life span of cause “oxidative stress” and can produce gene activity in the two groups of flies.” the fly.” H

HHMI BULLETIN 41 APRIL 2001 CLOSE-UP

the AD GEIS SANDY Artof science

HHMI Purchases the Geis Archive

“The Leonardo da Vinci of protein States. Working closely with scientists to structure” is how one scientist ensure accuracy, he produced images described Irving Geis, a pioneering whose beauty and power remain strik- artist who saw the splendor in biology’s ing even when compared with those molecules and helped countless scien- produced by modern computer graphics. tists and students envision how life is put together. In August 2000, HHMI Rights to all images owned and administered by the Howard B-DNA, 1984 purchased a large collection of Geis’s paintings, sketches and drawings and is Hughes Medical Institute. Reproduction by permission only. now displaying selected works at its headquarters and conference center in Chevy Chase, Maryland. A native New Yorker, Geis (1908–1997) earned an international reputation for his artistic innovations, particularly in depicting the structures of biological macromolecules such as DNA. Many of his illustrations appeared in Scientific American, includ- ing a 1961 painting of the protein crystal structure of myoglobin, the first such structure depicted. Geis illustrated numerous scientific textbooks, was a guest lecturer at universities and medical schools and exhibited his work at scien- tific institutions throughout the United

Crambin (detail), illuminated sulfur atoms, 1985

HHMI BULLETIN 42 APRIL 2001 Myoglobin with Bound Oxygen, 1984

Tomato Bushy Stunt Virus, 1984 CLOSE-UP

Diamond Ball and Stick Structure, 1978

Cytochrome C (hydrophobic side chains in red), 1988

HHMI BULLETIN 44 APRIL 2001 Genetic Code: A-T, C-G, 1993 Hemoglobin, 1984Artthe of science

Myoglobin Fold, 1987

Gap Junction, 1985

HHMI BULLETIN 45 APRIL 2001 OBJECT LESSON

Redesigning Laboratory Classrooms

By Ronald L. Rutowski and Allison Whitmer classrooms make this seem more trouble dents are learning about the nature of than it’s worth. science. We’re using questionnaires, How can students learn to work together At Arizona State University, we’ve been direct observations and other techniques as scientists when they’re stuck in thinking a lot about how to design labo- to assess the remodeling. H classroom laboratories that keep them ratory classrooms that facilitate lessons separated? based on personal inquiry and discovery. Ronald L. Rutowski is the managing That’s the dilemma science educators We’ve worked with specialists from our director and Allison Whitmer is the pro- face at many colleges and universities College of Architecture and Environmental gram manager of the Undergraduate across the country. They want students Design to redesign and renovate several Biology Enrichment Program at Arizona to collaborate on open-ended questions, classrooms. Already, we’re seeing improve- State University. just as scientists would in a research lab, ments in the ability of instructors to use but outdated, inflexible laboratory innovative pedagogy and in what stu- RONALD L. RUTOWSKI

Better classroom design does not require expensive high-tech furniture. Straightforward designs like this one, which we’ve adopted for several courses, also promote student collaboration. The modular table design is critical for encouraging interaction and enabling instructors to be flexible in the sizes of working groups.

HHMI BULLETIN 46 APRIL 2001 This is the new design for our cell biology lab.The biggest challenge was to build in equipment that is large and difficult to move, such as fume hoods, incubators and big microscopes with attached equipment for capturing and analyzing images.We were constrained by the “stationary footprint” of these tools. Enough floor space remained, however, to include areas where students can gather in small groups to collaborate on designing experiments and analyzing and interpreting data.

This old-fashioned laboratory classroom will look familiar to many readers. It has long tables, blocked sight lines, poor lighting, uncomfortable seating and other features that make it difficult for students to work together. It was designed at a time when students were expected to work individually on canned laboratory exercises with predeter- mined answers. ABR BACKES (3) BARBARA

Our first project was the renovation of a lab for a large course on human anatomy and physiology. Working with design consultants and classroom instructors, we used questionnaires and videotapes to analyze traffic patterns, clarify goals and come up with a new design.The lab’s most important feature is its small stations where students work together and have easy access to equipment and specimens.The students also have unobstructed views of the instructor’s station and each other, an arrangement that promotes classroom discussions and student-instructor interactions.

HHMI BULLETIN 47 APRIL 2001 INSIDE HHMI

for Biology Teachers has expanded Peter Bruns beyond Ithaca to all of upstate New York and to satellite operations in Manhattan, Seeks to Bind Boston, Hartford and Cleveland. Teachers work alongside Cornell scien- Science to tists during the summer to learn what’s new in biology and to develop hands-on Education lesson plans. The program also distrib- utes teaching kits, holds workshops at Peter J. Bruns, who was the driving force education meetings and assists teachers behind nationally recognized programs at throughout the school year. Cornell University for undergraduate Hunter R. Rawlings III, Cornell’s presi- research and outreach to high school dent, says Bruns “had a huge impact on teachers, has two important collections biology on this campus and throughout within steps of the office he is leaving the state of New York. He really does there. FETTERS PAUL care about people learning biology well.” The first is his freezer filled with After three decades in Ithaca, Bruns strains of Tetrahymena thermophila, the says he’s ready to move onto the national curious pond organism that Bruns has stage. He knows HHMI well, having studied for years to learn how two nuclei Bruns oversees HHMI’s grants and served as the program director for three in a single cell can have different roles special programs, which support science undergraduate education grants totaling yet work together to divvy up the vital education at all levels. $6.2 million—indeed, he credits the functions of life. Then, downstairs, is his Institute with expanding his own hori- room crammed with teaching kits on as a make-or-break function. I want to zons beyond the laboratory. “Frankly, DNA gel electrophoresis, immunology help change that nationally, just as we’ve those grants were one of the main and dozens of other topics, which Bruns done at Cornell.” Bruns emphasizes that reasons I got so heavily involved in and his colleagues share with high school his first priority at HHMI will be to education programs,” he says. teachers. assist the grantees, but he’s quick to add HHMI President Thomas R. Cech, Science and education are also the two that “I didn’t take this new job just to who has “known Peter as an outstanding nuclei of HHMI’s world, and Bruns has make people feel good”—words that scientist for many years,” says the been given the task of binding them more don’t surprise Cornell colleagues who Cornell geneticist emerged over the past closely together. Late last year, he was have seen the strong determination decade as “one of the country’s most cre- elected by the Trustees to become the behind his gentle demeanor. ative science educators.” In his new role, Institute’s vice president for grants and “Peter is terrific at turning bright ideas Bruns will continue searching for ways to special programs, overseeing activities into workable programs,” says Laurel better integrate research and education that complement HHMI’s primary mis- Southard, who oversees an array of and strengthen ties between scientists and sion of carrying out research with its undergraduate research programs at teachers—not only to educate future own scientific teams. Since 1987, the Cornell, several of which Bruns started. researchers but also to improve scientific Institute has awarded more than $1 bil- “He made some enemies by pushing so understanding among the public. lion for fellowships, precollege and hard for student research when he was He stresses that he will work closely undergraduate education programs, U.S. the director of the biology division here. with the HHMI staff, grantees and the research institutions and international But now, largely because of his efforts, broader scientific community to analyze science. high school students are applying to possible new initiatives rather than just “I want to lure more of the scientific Cornell because of these opportunities, replicate his work at Cornell. Pausing on community into education programs,” and faculty are coming because they his way home to Ithaca after completing Bruns says during a conversation in his want to teach as well as do research.” his first full week at HHMI’s headquar- small office overlooking the soccer field “Peter’s been able to change the cul- ters, he muses that “some of my friends at Cornell, where he’ll spend part of his ture, which is very difficult,” agrees Rita at Cornell have asked how I can give up time until he and his family move to Calvo, who teamed with Bruns to create doing experiments. I tell them that I used Maryland after the spring term. “Right a widely admired—and imitated—out- to do experiments in genetics; now I plan now, I don’t think that our research uni- reach program with high school teachers. to do experiments in education.” H versities value undergraduate education Launched in 1990, the Cornell Institute

HHMI BULLETIN 48 APRIL 2001 HHMI ONLINE

In the Lab

A new design has made it easier for visitors to HHMI’s Web site to learn about the Institute’s scientific programs. Clicking “In the Lab” on the home page (www.hhmi.org) leads to a screen offering information on HHMI’s international research scholars, advisory boards, laboratory safety program and intellectual property policies, and the HHMI-NIH Research Scholars Program for medical students. Most important, there’s extensive infor- mation about the nearly 350 HHMI investigators who carry out biomedical research across the United States. For each, the site provides a current research abstract, short biography and photo, as well as links to recent news stories about them, their per- sonal home pages and a listing of their recent publications on the National Library of Medicine’s PubMed Web site. Visitors can search the investigators by name, insti- tutional affiliation or topic. Rights owned and administered by the Howard Hughes Salt Crystal, 1978 Medical Institute. Reproduction by permission only.

Howard Hughes Medical Institute 4000 Jones Bridge Road Chevy Chase, Maryland 20815-6789 301.215.8855 www.hhmi.org