September 2011

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September 2011 ASBMB Today 1 president’smessage A monthly publication of The American Society for Biochemistry and Molecular Biology The importance Officers of mentorship Suzanne R. Pfeffer President Jeremy M. Berg President-Elect BY SUZANNE PFEFFER Mark A. Lemmon Secretary Merle S. Olson Treasurer Council Members Karen N. Allen Ruma V. Banerjee cientists become scientists by apprenticeship. We learn how to Dafna Bar-Sagi Benjamin F. Cravatt Michael A. Marletta David Sabatini S identify a question, design an experiment, publish and present our John D. Scott Wesley I. Sundquist findings, write a grant application and lead a team. We learn how to get Jonathan S. Weissman a job, keep a job and get promoted. We learn how to manage people Ex-Officio Members Russell DeBose-Boyd and hopefully how to inspire them. We learn how to deal with ethical Hongtao Yu issues, and we learn about our responsibilities as scientists. Appren- Co-chairs, 2012 Annual Meeting Program Committee Peter J. Kennelly tices need mentors to teach them all these things, and different kinds of Chair, Education and Professional Development Committee mentors are needed at each stage of our careers. It seems obvious that Joan W. Conaway junior scientists need mentors; senior scientists need them, too. Chair, Meetings Committee Terri Kinzy Teachers and research advisers are obvious mentors during under- Chair, Membership Committee graduate, graduate and postdoctoral training. The identification of Squire J. Booker Chair, Minority Affairs Committee mentors at later career stages is not always as straightforward. Some Bettie Sue Masters institutions assign mentors to junior colleagues to meet with them annu- Chair, Public Affairs Advisory Committee Charles Brenner ally (or more frequently) and provide feedback on how well they are Chair, Publications Committee meeting the requirements for promotion. Mentors can provide feedback Martha J. Fedor, Editor-in-chief, JBC on grant applications and project proposals and help with staff chal- Herbert Tabor, Co-editor, JBC Ralph A. Bradshaw lenges or lab-management issues. The best mentors can promote you A. L. Burlingame within the professional realm: They can recommend you as a speaker at Co-editors, MCP Edward A. Dennis a meeting, as a lead scientist on a project or as an author of a minireview Joseph L. Witztum for a prestigious journal. At later career stages, mentors can provide Co-editors, JLR advice regarding new job opportunities or administrative roles. They can ASBMB Today Editorial Advisory Board Alex Toker (Chair) help nominate you for awards and recommend you for other professional Mike Bradley Craig E. Cameron activities. They can offer advice about negotiating difficult situations or A. Stephen Dahms Alex C. Drohat Ben Ellington Irwin Fridovich transitions. The most successful scientists nurture informal relationships Richard W. Hanson Gerald Hart with multiple mentors. Just knowing that one has wise counsel and sup- Peter Kennelly Carol C. Shoulders port from colleagues is important at every stage. ASBMB Today Angela Hopp Interim Editor [email protected] My mentors Erin Salb Production Coordinator I feel very lucky to have had wonderful and incredibly generous mentors [email protected] throughout my career. Nancy J. Rodnan Director of Publications [email protected] Barbara Gordon Executive Director When I was an undergraduate at the University of [email protected] California, Berkeley, my mentor, Michael Chamberlin, For information on advertising, contact took time to show me how to write an experimental Capitol Media Solutions at 800-517-0610 protocol and a scientific paper. His writing skills were or [email protected] inspiring. I was drawn to Mike’s lab because of the passion with which he described his research question: He wanted to understand how RNA polymerase www.asbmb.org/asbmbtoday Chamberlin selected a promoter to initiate transcription. I remember very clearly my first visit to his office to find out if he had space for an undergrad. He took to the chalkboard to draw out the location of

2 ASBMB Today September 2011 president’smessage

promoter sequences on T7 bacteriophage DNA. They come in many forms Chamberlin respected anyone who was 100 percent Mentors include advisers with career experience committed to his or her science, undergrads included. willing to share their knowledge, supporters who He regaled his lab members with tales of and provide encouragement, tutors who give performance , his own mentors. All of us learned feedback, sponsors who help open opportunities, what Arthur (apparently) would have done if he found and models of identity (1). Although at the time there someone reading a newspaper during lab hours. were very few (if any) women in the departments in which I trained, I have benefitted from wonderful role My Ph.D. adviser at the University of models whom I came to know through membership California, San Francisco, Regis in scientific societies and participation on extramural Kelly, was also a Kornberg mentee — committees. , Joan Steitz, Liz Black- and he taught me the importance of burn, , Heidi Hamm and Carla Shatz identifying a fundamental, unanswered have impressed me with their tremendous leadership question. When I joined Reg’s lab, they and diverse individual styles. were deep into analyzing the protein Most recently, Greg Petsko has been an outstand- Kelly and lipid composition of synaptic ing mentor to me; working with Greg has been a vesicles purified from electric rays and just beginning to real highlight of my term as ASBMB president. From study the mechanisms by which peptide hormones are Greg, I have learned the importance of speaking out sorted for regulated secretion. Reg gave lab members a for what you believe in. Greg has an unusual com- great deal of independence to conquer their projects mitment to the people with whom he works, and he and adopt the science as their own. In his lab, I learned has earned a devoted fan club of scientists around the importance of sharing and discussing all the lab’s the world. I will do my best to continue to nurture science among all lab members. He shared with Greg’s mentorship in the years to come, and there is Chamberlin a great enthusiasm for science, and he no question that I also have much to learn from our pushed me to be fearless to do that key experiment incoming president-elect, Jeremy Berg. More junior that would either prove a new model or rip it to shreds. colleagues also can be great mentors, and Pehr Har- Reg encouraged fearlessness in multiple arenas: Few bury and I mentor each other here in the biochemistry could match his skills when the entire lab would take a department at Stanford. day for skiing at Squaw Valley or whitewater rafting and Mentee-mentor relationships can bring great kayaking on a nearby river. rewards to both partners. To those of you who men- tor others, the act of mentoring honors your own My postdoc mentor at Stanford mentors. Mentees, remember that there are many University, Jim Rothman, did not people around you who can provide invaluable train with Kornberg, but Kornberg advice, guidance and support at critical junctures. was one of his heroes. When I joined Seek those people out and develop those relation- the Rothman lab, they had just ships. To all of my mentors, past, present and future, established the first cell-free system mentioned or not, thank you! that reconstituted the transport of a Rothman viral glycoprotein from one compart- ASBMB President Suzanne Pfeffer (pfeffer@ ment of the Golgi to the next. There, I learned how to stanford.edu) is a biochemistry professor at establish a cell-free assay for a membrane-trafficking the Stanford University School of Medicine. event and how to try to obtain precise molecular

information from such complex mixtures. Rothman

showed me the value of strategy sessions to coordinate

lab member contributions to achieve specific goals

expeditiously. Rothman is a masterful orator, and I tried REFERENCE to learn from him how to grab and command an 1. Making the right moves: a practical guide to scientific management for audience’s attention during a lecture. postdocs and new faculty. At http://www.hhmi.org/labmanagement.

September 2011 ASBMB Today 3 asbmbnews Retrospective: Nathan Sharon (1925 – 2011) BY EVE IDA BARAK AND EUGENE A. DAVIDSON

athan Sharon, a lifelong ambassador for lysis compared with the rate of ant walking. N science and an accomplished glyco- Although this study had nothing to do with scientist, died June 17. He was 85. , it can be reasoned that Sharon was born in 1925 in Sharon appreciated Koshland’s creativ- and immigrated to (then the Brit- ity, a trait he too demonstrated as ish Mandate for Palestine) in 1934 at he asked (and answered) many key age 8. Later, he became involved in questions in the saccharide field. the military struggle for Israeli inde- Broad interests in natural phe- pendence and served in the science nomena were a hallmark of Sharon, corps of the . and he was drawn to an old find- He earned his bachelor’s and doctor- ing about cell aggregation. The first ate in from Hebrew Univer- observations that some naturally sity and in 1954 joined ’s occurring molecules (agglutinins) biophysics department at the Weizmann cause types of cells to aggregate date Institute of Science, where he remained for to the late 19th century. This phenom- his entire career. enon remained for decades in the category Sharon started out working on bacterial poly- of “interesting observations,” with little known peptides. In 1956, he went to to learn about the nature of the interacting species, the mecha- more about peptide biosynthesis from Fritz Lippmann nism or the basis for the apparent specificity. Unravel- and consulted with Roger W. Jeanloz about a polysac- ing this puzzle became Sharon’s lifework. He defined charide he found in a Bacillus (none was known then). the molecular nature of the saccharide recognition and Jeanloz urged him to publish his findings in Nature and was a founding father for the general area of cell-cell invited him to Boston to characterize the polysaccharide recognition. chemically. This resulted not only in the discovery of In addition to maintaining a world-class research pro- novel bacterial sugar bacillosamine (2,4-diamino-2,4,6- gram, Sharon was active in administrative affairs, trained trideoxyglucose, which has been implicated as the link numerous successful investigators and brought science in N-linked glycosylation of bacterial proteins), but it to the public as science editor of the Haaretz newspaper launched his career in complex carbohydrates. and editor of a radio broadcast on science. Perhaps less known to the glyco community is his To Sharon, science was personal. His travels took him work with Daniel E. Koshland Jr. at Brookhaven National all over the world to get to know his fellow glycoscien- Laboratory. The paper that resulted in the Proceedings tists personally. Those who knew him will always remem- of the National Academy of Sciences had an unusual ber his personal warmth and graciousness. title: “Purified muscle proteins and the walking rate of ants.” Not exactly glycobiology! The study tested William Eve Ida Barak (ebarak@alumni. J. Crozier’s 1924 hypothesis suggesting that in specific brown.edu) is a former (now physiological processes a single enzymatic reaction retired) program director for served as the rate-determining step, and this control cellular biosciences at the was exerted over a sufficiently broad temperature range National Science Foundation and to assess the activation energy of the reaction. Sharon Eugene A. Davidson ([email protected]) is a professor and Koshland used purified myosin and live ants and emeritus in the department of biochemistry and molecular and measured temperature effects on the rate of ATP hydro- cell biology at the Georgetown University School of Medicine.

4 ASBMB Today September 2011 asbmbnews Retrospective: Saul Roseman (1921– 2011) BY RONALD L. SCHNAAR AND GEORGE W. JOURDIAN

aul Roseman, professor emeritus at The transferase activities in tissues and bodily fluids. SJohns Hopkins University, died peace- During a summer stint in H. Gobind fully July 2 after a career in science of Khorana’s lab, Roseman devised a nearly 70 years. He had profound chemical means to synthesize sugar effects on the field of glycobiology and . The availability of these our understanding of bacterial sugar compounds in large amounts let inves- transport. His enthusiasm and inten- tigators study the biosynthesis of the sity were prodigious and contagious. oligosaccharide chains of glycopro- He leaves a distinguished legacy of teins and glycolipids. discovery. Roseman and his team were Roseman earned a bachelor's in exploring the of N-acetyl- 1941 from City College of New York. mannosamine by bacteria when they He earned his Ph.D. in 1948 under Karl stumbled upon a finding that provided Link at the University of Wisconsin. His new insights into bacterial sugar transport. doctoral pursuit included a hiatus to serve As one of the controls for ATP-dependent as an infantryman in World War II. During post- hexosamine phosphorylation by Escherichia doctoral studies at the University of Chicago with coli, phosphoenolpyruvate was added. Surprisingly, Albert Dorfman, he studied glycosaminoglycans, initiating bacteria failed to transfer phosphate from ATP to ManNAc a lifelong interest in hexosamine metabolism. In 1953, he but robustly transferred phosphate from phosphoenolpyru- joined the Rackham Arthritis Research Unit at the Univer- vate. Eventually, the team purified and characterized the sity of Michigan Medical School as an assistant professor. bacterial phosphotransferase systems that simultaneously At Michigan, his research initially concentrated on transport and phosphorylate sugars. The biochemistry, the metabolism of sialic acids, prominent cell-surface thermodynamics and function of the PTS were explored determinants and among the most abundant sugars that vigorously. Later, Roseman focused on the roles of glycans terminate the oligosaccharide chains of glycoproteins in cell-cell recognition and chitin metabolism by Vibrio and and glycolipids. Within a short time, he and postdoctoral other bacteria. His lab continues to pursue these goals, researcher Don Comb convincingly proved that sialic acid and Roseman had hoped to make substantial contribu- contained N-acetylmannosamine, an unexpected find- tions well into his 10th decade. He never lost his enthusi- ing because numerous investigators had concluded the asm and passion for the next experiment. hexosamine constituent of sialic acid was N-acetylglu- Roseman’s seminal discoveries often were character- cosamine. Roseman’s manuscripts reporting the correct ized as serendipitous, because both the correct struc- structure of sialic acid were clear, rigorous, thorough and ture of sialic acid and the PTS system were unexpected compelling, a style of research and communication that findings. Of this, Roseman once said: “The unexpected remained a hallmark. is just nature’s way of telling researchers where to look The finding initiated a remarkably productive period of for the really interesting and important stuff.” Interesting, seminal discoveries in the Roseman lab, including path- indeed! ways for the biosynthesis and degradation of sialic acids, isolation and characterization of CMP-sialic acid and Ronald L. Schnaar ([email protected]) is a professor at The Johns its demonstration as the sugar donor for the Hopkins School of Medicine, and George W. Jourdian (gjourdia@ biosynthesis of sialylated glycans, enzymatic pathways for med.umich.edu) is a professor emeritus at the University of hexosamine biosynthesis, and characterization glycosyl- Michigan Medical School.

September 2011 ASBMB Today 5 asbmbnews Annual award winners named Outstanding scientists to be honored at the annual meeting. BY SNEHA RAO

he American Society for Bio- Susan Marqusee, metabolism of phospholipids, and, Tchemistry and Molecular Biology a professor at the most recently, his laboratory discov- in July named 12 scientists the University of Califor- ered the molecular function of the winners of its annual awards. The nia, Berkeley, and fat-regulating protein lipin as a phosphatidic acid phosphatase newly announced recipients and one director of Berkeley’s California Institute for . winner from 2011 will give talks at Quantitative Biosciences, has been the annual meeting April 21 – 25 in Peter Espenshade, named the winner of the William C. an associate professor San Diego. Rose Award. The award recognizes at Johns Hopkins her outstanding contributions to Stuart Kornfeld, University School of biochemical and molecular biological a professor at Washing- Medicine, won the research, particularly in the field of ton University in St. Avanti Young Investi- protein folding, and her demonstrated Louis, won the Herbert gator Award in Lipid Research. commitment to the training of Tabor/Journal of The award recognizes outstanding younger scientists. Biological Chemistry research contributions in the area of Lectureship. The award recognizes Barry Honig, lipids by young investigators with no outstanding lifetime scientific achieve- Columbia University more than 15 years of experience ments and was established to honor the professor and Howard since receiving their doctoral degrees. many contributions of Herbert Tabor to Hughes Medical Espenshade researches the basic both the society and the journal, for Institute investigator, mechanisms of cholesterol sensing which he served as editor for nearly 40 won the DeLano and has developed the simple years and now serves as co-editor. Award for Computational Biosci- eukaryotic cell S. pombe as an ences for his work in macromolecular accessible genetic model for the Lovell Jones, interactions in biology. The award is investigation of cholesterol homeosta- a professor at both the given to a scientist for innovative and sis and is pursing the pathways University of Texas M.D. accessible development or application controlling this fundamental cell Anderson Center of computer technology to enhance process. and the University of research in the life sciences at the Houston as well as Peggy Farnham, molecular level. Honig’s software tools director of the joint Dorothy I. Height a professor at the and their underlying conceptual basis Center for Health Equity & Evaluation University of Southern are widely used by the general Research, won the Ruth Kirschstein California, won the biological research community to Diversity in Science Award. This award Herbert A. Sober analyze the role of electrostatics in honors an outstanding scientist who has Lectureship. The macromolecular interactions. shown a strong commitment to the award, issued every other year, encouragement of under-represented George M. Carman, recognizes outstanding biochemical minorities to enter the scientific enterprise professor and director and molecular biological research with or to the effective mentorship of those of the Center for Lipid particular emphasis on development of within it. Jones has been devoted to Research at Rutgers methods and techniques to aid in diversity issues in the scientific commu- University, won the research. Farnham studies chromatin nity, with a major emphasis on both Avanti Award in regulation and its control of transcrip- addressing the under-representation of Lipids. Carman, associate editor for tion-factor binding and function, and minorities at all levels in academia, the Journal of Biological Chemistry, she is a pioneer in the development of industry and government as well as health has made many contributions to the the chromatin immunoprecipitation disparities in the U.S. understanding of the enzymology and technique.

6 ASBMB Today September 2011 asbmb news ResouR ce: genomewide Xiaodong Wang, serine or threonine hydroxyl in mamma- a Howard Hughes lian Rho , inactivating these epigenetic Medical Institute alumni . Her studies bring new insights investigator and to the field of eukaryotic signaling. maps researcher at the Judith Voet, National Institute of professor emeritus at Researchers in the Reference Biological Sciences in Beijing, has been Swarthmore College, named the winner of the ASBMB-Merck Epigenome Mapping Consortium, and Donald Voet, Award. This award recognizes out- part of the NIH Common Fund’s associate professor standing contributions to research in at the University of Roadmap Epigenomics Program biochemistry and molecular biology. Pennsylvania, won the (http://commonfund.nih.gov/ Wang studies the functions of cell ASBMB Award for organelles and is credited with the epigenomics), have begun cre- Exemplary Contribu- discovery of a new function of mito- ating a community resource of tions to Education. chondria in programmed cell death. The Voets have made genomewide epigenetic maps in David Sabatini, significant contributions a variety of human primary cell an associate professor to the teaching of biochemistry and and tissue types. at the Massachusetts molecular biology through their writing. Together, they have authored the Institute of Technology The data represent more than and a Howard Hughes comprehensive textbook “Biochemis- Medical Institute try,” co-authored “Fundamentals of 100 samples, including adult investigator, won the Earl and Thressa Biochemistry” and co-edited the and fetal cells and tissues and Stadtman Scholar Award, given to educational journal “Biochemistry embryonic and induced-pluripo- a scientist with 10 or fewer years of and Molecular Biology Education tent stem cells. postdoctoral experience, including (BAMBED).” medical residency and fellowship. Christine Guthrie, Sabatini is a leader in the ongoing The majority of reference epig- a professor at the elucidation of the mTOR pathway, a enomes being generated contain University of California, master regulator of growth. He is also San Francisco, last year information about DNA methyla- a member of the Whitehead Institute won the ASBMB-Merck tion, a core set of histone modi- for Biomedical Research. Award, which recognizes fications, chromatin accessibility Kim Orth, outstanding contributions to research in and gene expression. a professor at the biochemistry and molecular biology. Guthrie, an American Cancer Society University of Texas A subset of reference epig- Southwestern Medical research professor of molecular genetics, Center at Dallas, has pioneered the use of budding yeast as a enomes also will contain an been named the winner model organism to elucidate the mecha- expanded set of at least 20 of the ASBMB Young Investigator nism of messenger RNA splicing. additional histone modifica- Award. Orth’s most notable achieve- tions. The consortium’s website ments include the discovery of novel Look for more in-depth cover- post-translational modifications age of the award winners and (http://roadmapepigenomics.org) exploited by the virulence factors their lecture topics in forthcom- provides information about pro- secreted by bacterial pathogens. One of ing issues of ASBMB Today and tocols developed by consortium these, YopJ from Yersinia, the causal at www.asbmb.org. agent of plague, transfers an acetyl members, information about data group from acetyl CoA to a serine or standards and links to a variety of threonine hydroxyl in mammalian MAP sites where the epigenomic data kinase kinase, inactivating the enzyme. Sneha Rao ([email protected]. can be visualized in a genome Another virulence factor, VopS from edu) is an undergraduate Vibrio parahaemolyticus, a cause of at the University of North browser or downloaded for sub- debilitating diarrhea, is an enzyme that Carolina at Chapel Hill. sequent analysis. AMPylates (transfers AMP) to tyrosine,

September 2011 ASBMB Today 7 news from the hill Here we go again BY BENJAMIN CORB

ave you heard the latest attacks on peer-reviewed Hscience? Whether it’s criticisms from well-respected We’re here to serve you interest groups or from fringe elements with specific social agendas, it seems that, everywhere you turn, peer review in agencies such as the National Science Founda- tion and National Institutes of Health is being questioned. As groups grapple over a shrinking pile of federal dol-

lars, once-sacred areas of investment, including basic Benjamin Corb Geoff Hunt Julie McClure biomedical research, have become political fodder for Director of Policy Fellow Policy Fellow both sides of the aisle. Your public affairs staff at the Public Affairs [email protected] [email protected] [email protected] American Society for Biochemistry and Molecular Biology headquarters has been working diligently to dispel and debunk rumors, innuendo and out-and-out lies by con- unfair critiques of the research enterprise in general or the ducting more than 40 meetings with members of the U.S. peer-review process specifically, take a minute to set the House since the summer began. But we need your help. record straight by making a phone call. Don’t know whom Here are some things you can do to help take the politics to call or what to say? Contact us, and we’ll provide you out of science. with info, encouragement and support. Talk about your research. Whether it’s in line at What do elected people want to know about? the grocery store, at a ballgame or at the bake sale after Probably not DNA methylation. But talk about what your church, strike up conversations about your science. Did research could yield. Talk about the people employed in you know that one in four Americans cannot name a your lab, department, university or company. Talk about scientist? And half of Americans, when asked to name a how you use your grant funds strategically and efficiently. scientist, could name only Albert Einstein. Surely, Einstein Talk about the lives that may be saved or changed. was great, but with 12,000 members in the ASBMB Work with the ASBMB public affairs staff. Our alone, our neighbors should know scientists. team is scientifically aware (thanks to the policy fellows I’m not asking you to discuss post-translational modi- and 15-member Public Affairs Advisory Committee) and fication or cell-signaling cascades. I’m suggesting you get politically astute. We meet with members of Congress, comfortable talking about the potential outcomes of your the administration and with partner organizations. One work. Will it help scientists understand molecular mecha- thing we’re not is everywhere. If you see an example of nisms that may one day lead to cures? Will it reduce the science being politicized, let us know about it. If you’d like occurrences of birth defects or make a terminal disease to host a lab tour for your representative, we’d be happy a chronic one? Help the public know that science is well to help with that as well. If you want to write a letter to intentioned and promising so that, when criticisms are the editor of your local paper, we’ll help you through the made in the public sphere, family members, friends and process, from editing to getting it placed for publication. neighbors will defend the importance of research. As Congress battles over funding levels and pro- Get involved politically. No, I’m not asking you to poses massive cuts to everything from defense to social become a fat-cat donor. And I’m not asking you to rack programs, we will continue to see the politicization of sci- up frequent-flier miles to roam the halls of the Capitol. ence. The best— and, frankly, the only— way to preempt (That’s my job!) I’m asking you to find out who represents or thwart these attacks is to put up a strong defense. you in Congress and to call, write or email him or her You, with your years of experience and understanding when an issue comes to your attention. Politicians are of the scientific enterprise, provide us in Washington not always as narcissistic as we think, and they need to with the best ammunition to keep politics out of the hear from the people they represent. If you hear about laboratory.

8 ASBMB Today September 2011 UASBMB UndergraduateN Affiliate Network 2010-2011 MEMBERSHIP DRIVE Renew Your Membership Today! • Travel awards to the 2012 ASBMB Annual Meeting in San Diego, CA • Free online subscriptions: Journal of Biological Chemistry Molecular and Cellular Proteomics Journal of Lipid Research • Free online and print subscription to ASBMB Today, the society magazine • ASBMB-sponsored research awards and scholarships exclusively available to UAN

Member Benefits students • Nomination into the ASBMB Biochemistry and Molecualr Biology Honor Society

Check us out at: www.asbmb.org/UAN

Membership Drive Flyer2012.indd 1 8/25/2011 11:13:30 AM asbmbnews Targeting carriers of infectious tropical disease BY ANGELA HOPP

hun-Hong Chen, an assistant investigator at the His postdoctoral C National Health Research Institute in Taiwan, won a training was completed Journal of Biological Chemistry/Herbert Tabor Award for under the direction his work with engineering disease-refractory mosquitoes of Bruce Hay at the to prevent transmission of dengue fever. California Institute of A native of Pingtun county, Taiwan, Chen applied a Technology in Pasadena. Together, Hay and Chen cre- microRNA-based RNAi system to knock down multiple ated a gene drive system for population replacement dengue virus genomes in the yellow fever mosquito in a Drosophila model. In 2009, Chen returned to his Aedes aegypti. homeland and joined the National Health Research “Although there are several steps to go, if we can Institutes in Zhunan Town. combine the resistant mosquito with a gene drive sys- tem, we will have an alternative way to fight against such vector-borne disease,” Chen says. Chen earned his bachelor’s and master’s degrees in plant virology at National Taiwan University and his Ph.D. at National Yang-Ming University, where he worked with Soo-Chen Cheng on RNA splicing.

Chun-Hong Chen received his award at the Recent Advances in Pathogenic Human Viruses special symposium held July 24 – 26 in Guangzhou, China. The meeting was co-sponsored by the American Society for Biochemistry and Molecular Biology and attended by Journal of Biological Chemistry Editor-in-Chief Marty Fedor and Associate Editor Charles Samuel. PhoTo CourTESy oF WEn-Ling ChEn.

10 ASBMB Today September 2011 asbmbnews

Amy Walker received her award at the 52nd International Conference on Harvard the Bioscience of Lipids, which was held July 17 – 22 in Waterville Valley, med school N.H., and attended by JBC Associate Editor George Carman. investigator PhoTo CourTESy oF JoESEPh FErrAro. and 1-carbon metabolism recognized is related to mechanisms of BY ANGELA HOPP transcription factor function, such as the sterol regulatory my Walker, an instructor at Harvard Medi- elements binding proteins,” cal School and the Center for Cancer A she says. Research at Massachusetts General Hospital, A Mobile, Ala., native, Walker received the Journal of Biological Chemistry/ completed her undergradu- Herbert Tabor Award for her studies of how ate studies in microbiology at metabolic pathways are linked to transcrip- Auburn University, graduate tional programs and other aspects of cell studies in molecular microbiol- biology. ogy at the State University of New York, Stony Brook, and “In my graduate and postdoctoral work, my primary postdoctoral training at Harvard Medical School. interest was how transcriptional activators and the basal transcription machinery played roles in specific develop- mental processes,” Walker says. Angela Hopp ([email protected]) is a science Today, Walker and colleague Ander Näär focus on writer and handles public relations for ASBMB. links between transcriptional regulation and lipid produc- tion. “In my lab, I use a combination of C. elegans and mammalian models to understand how regulation of lipid Sharing made easy Try out various social-bookmarking options when visiting ASBMB journal sites.

September 2011 ASBMB Today 11 asbmb member update

SCHEKMAN CORKEY MIYAZONO TANIGUCHI COLMAN HERBERT

Schekman tapped significant, long-term contributions to the Miyazono was given the prize for as the top editor understanding of diabetes, its treatment or his achievements in identifying various its prevention. functions of TGF beta in cancer. For the of a new journal A leader in the fields of metabolism, past 25 years, Miyazono has made great Randy W. Schekman, a Howard Hughes diabetes and obesity for more than 35 strides in signaling mechanisms in cancer Medical Institute investigator and editor of years, Corkey works on the molecular cells. His most notable accomplishments the Proceedings of the National Acad- basis of nutrient and include identifying various functions of emy of Sciences, will lead the launch of a has improved significantly our understand- TGF beta in cancer and revealing their new open-access journal established by ing of health and disease. She developed signaling mechanisms and biological HHMI, the Max Planck Society and the the concept of glucolipotoxicity, in which functions. Wellcome Trust. elevated glucose and lipids cause tissue Schekman, a professor at the malfunction in diabetes, and found that Colman recognized University of California, Berkeley, has anaplerosis, malonyl-CoA, reactive oxygen devoted the past three decades to better species and long-chain acyl-CoA esters for her outstanding understanding the molecular machinery are linked to fuel metabolism and control publications, impact that enables proteins to be trafficked within of insulin secretion in beta cells. Roberta Colman, professor emeritus at cells. He has made many contributions the University of Delaware, was ranked in his field, including discovering how Two JBC board 23rd in the list of journal Biochemistry’s vesicles bud off from the cell’s endoplas- members receive 50 most prolific authors. Colman was mic reticulum and transport proteins and Japanese prizes one of only four women included in the identifying more than 50 genes involved in distinguished group. the process with his colleagues. Journal of Biological Chemistry edito- Her research focuses on understand- Schekman’s important role has yielded rial board members Kohei Miyazono ing the catalytic activity of enzymes in several major awards, including the and Naoyuki Taniguchi were selected terms of protein structure. Colman’s Albert Lasker Award for Basic Medical to receive the Japan Academy Prize. lab studies the enzyme glutathione Research, the Gairdner Foundation One of the most prestigious prizes in S-transferase, which plays an important Japanese academia, the Japan Academy International Award and the Louisa Gross role in detoxifying foreign chemicals, and Prize is given to nine recipients who have Horwitz Prize. adenylosuccinate lyase, a shortage of made great contributions in their respec- which is related to mental retardation and tive fields. The recipients come from a Diabetes group’s autism. wide range of academic fields, includ- Colman was ASBMB’s Herbert A. Banting award ing humanities, social sciences, formal Sober Award winner in 1996. goes to Corkey sciences, natural sciences and applied Barbara E. Corkey, vice chair of research sciences. IN MeMoRIaM in the department of medicine at Boston The Japan Academy Prize recognized University School of Medicine and director Taniguchi for his pioneering accomplish- Yoshito Kaziro of the Obesity Research Center at Boston ments in glycobiology and his discovery of Yoshito Kaziro, a longtime ASBMB mem- Medical Center, received the American the significance of N-glycans in disease. ber, passed away June 29 after a long Diabetes Association’s 2011 Banting His current research aims to study glycan- battle with lymphoma. The son of famous Medal for Scientific Achievement Award. related and infectious diseases researcher Kozo Kaziro, Named after Nobel Prize winner through multiple approaches combining Yoshito Kaziro studied under Sumio Frederick Banting, this prestigious award glycobiology, chemical biology, structural Shimazono, a leader in vitamin biochem- honors an individual who has made biology and bioinformatics. istry at the University of Tokyo. In 1959,

12 ASBMB Today September 2011 asbmb member update Please submit member-related news to [email protected].

Scenes from the special symposia The 2011 American Society for Biochemistry and Molecular Biology Special Symposia Series kicked off in July with meetings held in Guangzhou, China, and Richmond, Va. The Symposia Series continues with four fall meetings scheduled for September and October. To learn more about the Special Symposia Series, visit www.asbmb.org/ specialsymposia.

Journal of Biological Chemistry Editor- in-Chief Martha Fedor and Associate Editor Charles Samuel talk to keynote Suh-Chin Wu of National Tsing Hua University in Tai- speaker Michael M. C. Lai of Academia wan presents his poster at the “Recent Advances in Sinica and Ping Zhang of Sun Yat-sen Pathogenic Human Viruses” meeting at the Guang- University, Zhongshan School of zhou Baiyun International Convention Center. The Medicine, at the “Recent Advances in meeting was organized by Kuan-Teh Jeang of the Pathogenic Human Viruses” meeting in National Institute of Allergy and Infectious Diseases Guangzhou, China, held July 24 – 26. and Douglas Lowy of the National Cancer Institute. PhoTo CourTESy oF JLynn FrAziEr PhoTo CourTESy oF JLynn FrAziEr

About 100 people attended the education symposium “Student-Centered Education in the Molecular Life Sciences II” at the University of Richmond from July 20 – 23. The meeting was organized by J. Ellis Bell. PhoTo CourTESy oF JESSiCA BELL

he joined the laboratory of degree in chemistry and mathematics. He Ridge Institute for Medical Research at New York University, where he purified received his Ph.D. in physiological chem- and professor emeritus at Louisiana and crystallized -dependent pro- istry from the Johns Hopkins University State University Health Sciences pionyl-CoA carboxylase. Kaziro had the in 1964. Ackers joined the faculty at the Center, passed away June 22 at the opportunity to establish his own lab in the University of Virginia before returning to age of 70. Herbert was born Aug. 2, U.S. but instead returned to the University Johns Hopkins University as a professor 1940, in Hammond, La. He gradu- of Tokyo in 1963. His research focused on of biology. He then became the biochem- ated from Rhodes College and then GTPases functioning in translation and in istry department head at Washington received his Ph.D. in biochemistry in cell signaling. In 1992, he was appointed University School of Medicine. Ackers was 1967 from Louisiana State University president of Sanyo Gakuen University. instrumental in establishing the molecular Health Sciences Center. Herbert spent Recently, Kaziro mentored young life sci- biophysics program and expanding the the entirety of his career at LSUHSC entists at Kyoto University. department of biochemistry and molecular teaching and researching biochem- biophysics. He was known for his sense istry and molecular biology. Herbert’s IN MeMoRIaM of humor and his many contributions in main research interests included the Gary K. Ackers biophysics. intermediary metabolism of amino Gary K. Ackers, professor emeritus at the acids, amino acid nutrition, uric acid Washington University in St. Louis, died IN MeMoRIaM production and excretion, and gout. May 20 at the age of 71. Born in Dodge Jack D. Herbert He was known for his distinctive City, Kan., Ackers attended Harding Jack D. Herbert, founding member lecturing style and his love for New College and earned an undergraduate of the board of directors of the Blue Orleans’ culture.

September 2011 ASBMB Today 13 asbmbnews New faces and initiatives The Undergraduate Affiliate Network remains committed to shaping well-rounded grads. BY MARILEE BENORE

s researchers and educators, we under- A stand the need for an academically About the new UAN chair rigorous curriculum for undergraduates studying biochemistry and molecular biology. Undergraduate training also should include opportunities for students to broaden and deepen their education through research and to engage in networking, leadership and community-service activities. The ASBMB recognized the importance of the co-curricular experience by founding and supporting the Undergraduate Affiliate Network, a community of students and faculty members actively engaged in undergraduate biochemistry and molecular biology education and research. Supported by and working with the ASBMB Education and Professional Devel- opment Committee, UAN provides its mem- bers funding for research, travel and outreach projects and recognizes outstanding students Marilee Benore is a professor of biology and biochemistry and and chapters through its honor society and associate dean at the University of Michigan-Dearborn. She is active the UAN Outstanding Chapter Award. UAN in mentoring undergraduates, especially women and minorities, and faculty advisers are also supported through in conducting biochemistry education research. Benore has been a member of the ASBMB Education and Professional Development this network of educators and receive ample Committee, a co-chair of the undergraduate poster competition and opportunities to network at UAN regional a founding member of the UAN committee. She has served as a UAN meetings and at the ASBMB annual meeting. regional director and, for the past few years, as the editor of the UAN News and best practices across the UAN newsletter, Enzymatic. She is a co-author of a lab manual titled “Fun- community are shared through the UAN news- damental Laboratory Approaches for Biochemistry and Biotechnol- letter, Enzymatic. This year, Rebekah Waikel ogy” and offers workshops on service learning and outreach and on of Eastern Kentucky University takes over incorporating diversity issues into the biochemistry curriculum. as the chief editor. She will be implementing some changes to the newsletter while pre- serving popular features, such as JBC in the Classroom, service-learning course guidelines munity. Members from UAN chapters will get to work and career articles. Enzymatic is available on the with those on other campuses. Given the distinctive ASBMB website. cultural differences of schools across the country, A new pilot project this year called UAN BOSS, for students will get “glocal” practice while working on Borderless Outreach Strategies for Students, will bring a common theme. This year’s theme is nutrition and together UAN chapters across the country to develop food security. Look for details of the BOSS project in outreach projects and form a lateral support com- the next issue of Enzymatic.

14 ASBMB Today September 2011 asbmbnews

As the new chair of the UAN, my goals this year Want to get http://www.surveymonkey. are to engage my fellow UAN faculty members to com/s/Q2DB9VM. expand the network, to recruit new members and involved in UAN? • Contribute an article to to help members take full advantage of all the UAN • Start an undergraduate Enzymatic about resources. affiliate network chapter on • your experiences in your campus. outreach or service • Support your campus UAN learning, group by picking up the • unique courses, $200 membership tab. • cool projects, • Volunteer to judge • how you use the Journal undergraduate posters at the of Biological Chemistry in ASBMB annual meeting. your classroom, • Post a copy of the • alternate careers or Enzymatic newsletter on • video reviews. your office door. • Contact UAN at • Take the Enzymatic survey at [email protected].

been implemented to plug the leak, Theil says. We need your input “We hope that the new survey data will document marked improvement and also identify barriers that exist Take one of the ASBMB today so that new solutions can be forged,” she says. surveys evaluating gender The second survey was designed for all ASBMB issues in academic science members to assess the role of gender and family issues in career development, promotion and mentoring. Comple- BY ANGELA HOPP tion should take about 10 to 15 minutes, and participants can enter a drawing for a $25 Amazon gift card. n American Society for Biochemistry and Molecular Both surveys were created in collaboration with Altshu- A Biology task force has launched two surveys about lerGray, a strategic consulting firm that serves biomedical the roles of gender and family in the lives of biochemistry research enterprises. and molecular biology faculty members. Appointed by ASBMB President Suzanne Pfeffer, the Led by Elizabeth C. Theil of Children’s Hospital Oakland task force also includes Melanie H. Cobb of the University Research Institute, the task force designed the first survey of Texas Southwestern Medical Center at Dallas, Judith P. for department leaders to collect information about the Klinman of the University of California, Berkeley, Frederick R. gender composition of both programs and candidates for Maxfield of Weill Medical College of Cornell University, Janet academic positions advertised between 2005 and 2010. L. Smith of the University of Michigan Medical School, and “These new numbers will build on and contrast with JoAnne Stubbe of Massachusetts Institute of Technology. an informal analysis ASBMB conducted in 1986,” Theil The surveys will remain open through the end of explains. “That data made clear that a disproportionately September. small number of female ASBMB members held faculty positions.” Angela Hopp ([email protected]) is a science In the decades that have followed, the loss of writer and handles public relations for ASBMB. women from the academic science pipeline has been widely documented, and various mechanisms have

Survey for department and program leaders: www.surveygizmo.com/s3/577904/ASBMB-Dept-Chair-Survey. Survey for all ASBMB members: www.surveygizmo.com/s3/578661/Survey-on-Gender-and-Family-Issues.

September 2011 ASBMB Today 15 featurestory Students on the front lines of public engagement Harvard’s Science in the News program includes a variety of outreach activities and is being held up as a model. BY MORGAN THOMPSON

hen the H1N1 outbreak topics recently covered in the media. Slenn reports audi- Woccurred in 2009, Jeff ence sizes currently range from 150 to 250 people per Teigler was starting a graduate lecture, with about 30 attending post-lecture tours of program in virology at Harvard the medical school’s labs. In addition, SITN provides a Medical School. biweekly e-newsletter, “I was the only person the SITN Flash, interested in viruses that most written and edited by of my friends and family knew. students. In answering their questions — In 2009, SITN What is swine flu? How is it expanded its effort to worse than regular flu? Why include participation can’t I just ask for antibiotics from my doctor? — in the Cambridge Sci- I realized how big the gap was between scientists’ ence Festival, high- understanding and how that translated into public school outreach, and knowledge about something as common as our its own science café, yearly encounter with influenza,” Teigler says. Science by the Pint. Later that year, Teigler co-presented a public lecture at “Providing varied programming gives eager SITN vol- Harvard Medical School on swine flu, and today he helps run unteers a chance to share their love of science in a manner a program that focuses on scientific literacy. of their choosing,” Teigler says, “but it also attracts and Science in the News, a volunteer organization at Harvard engages audience members of different ages, interests and University, was founded in 1999. Teigler has been co-director backgrounds.” since January 2010, and Tammy Slenn joined him at the helm in January 2011. Motivated audience Teigler describes SITN’s mission as having three goals: 1) Some audience members, like Michael Shapiro, say they to fill the gap in access to science information after formal attend SITN lectures for professional development. education, 2) to address cases of widespread misinformation “I am a mathematician by training and a mathematical and misunderstanding of science, and 3) to create an avenue biologist by trade. That means that my general biological for direct communication between scientists and the public. education is full of holes and makes the SITN talks ideal for “Graduate students already harbor a desire to share their me,” Shapiro explains. “They start at a very elementary level passion for science,” Teigler says. “SITN taps that enthusiasm, and almost always teach me something I didn’t know.” giving students varied outlets to communicate science that Many participants are educators who want to stay cur- match their interests.” rent with cutting-edge science to bring back to their class- rooms, provide their students with examples of early-career A decade of growth researchers and receive professional-development credits. SITN first started as and continues to hold a free, public High school biology teacher Mary Ann Scheiner uses lecture series each fall at which teams of three graduate SITN’s newsletter in her classes. “Most of my students don’t students give two-hour, interactive talks on broad scientific really know what scientific research is. It’s great when I can

16 ASBMB Today September 2011 featurestory Initiative rewarded SITN offers volunteers autonomy to start new initiatives with the organization’s support, explains co-director Slenn, who developed Science by the Pint, the SITN science café, at which scientists give brief introductions to their research and answer attendees’ questions about their work and the life of a scientist while mingling at a bar. Middle school biology teacher Mike Hansen says he attends Science by the Pint to “stay abreast with what is happening on the front lines of science.” The events “allow me to be connected with researchers who I can hold up as exemplars to my students, as well as providing an excuse for a good pint or two,” Hansen says. “The information I get at these get-togethers deepens my knowledge and provides relevancy to material that is part of my curriculum — and it’s a fun time.” Slenn’s interest in reaching out to a broader, adult audience comes from personal experience. “I come from a town of blue-collar workers, teachers and a few businessmen, and I wanted to share the excitement of science with people who may not enjoy the lecture format,” she says. “Talk- ing to the public about my work reminds me of what excited me in the first place and helps me focus on big-picture implications of my research.” Today, 80 graduate students participate in one or more programs annually. Teigler says the most- cited reason for participation remains the satisfac- tion of applying specialized scientific training to serve others and give back to the community that supports the work. “However, SITN volunteers also A young participant peers down the microscope at zebrafish larvae at gain practical benefits from the focus on high-qual- Science in the News’ Model Organism Zoo at the 2011 Cambridge Science ity oral and written science communication,” he Festival. The exhibit explores fundamental genetic concepts of genotype says, “which provides useful training and résumé- and phenotype with the help of SITN volunteer “zoo handlers” and a selection of wild-type larvae and mutants with striking visual phenotypes. building opportunities for early-career researchers.” Recently, in collaboration with Harvard sci- ence faculty members and Nancy Houfek of the find something to catch their interest — and they realize that American Repertory Theater, SITN established a they could be doing something like that in just a few more graduate-level short course called Science Presentation as a years,” Scheiner says. Performing Art. Lecture attendee James Yakura lauds the graduate stu- Houfek distills theater techniques that aid effective science dents’ motivation and enthusiasm: “The lectures are timely communication in an interactive workshop for faculty and and understandable by anyone who has an interest in the staff members, postdoctoral researchers and students. Gradu- topic, the instructors are knowledgeable and radiate excite- ate students who take the course for academic credit have ment for their work, and the times are convenient to those of small-group follow-up sessions with science faculty members us with day jobs.” to hone the delivery of their presentations.

September 2011 ASBMB Today 17 firstfeaturesecondstory continued continued

A good example “We realized that it was not possible or desirable to When students at Yale University’s chapter of Scientists import the Harvard program wholesale. There are infra- and Engineers for America heard of SITN’s program, they structure disparities between the Harvard group and ours, decided to start their own lecture series, which they launched the differences between Boston and New Haven, and [our] this spring. mission, which leads us in a more policy-oriented direction,” “We were impressed by [SITN’s] scope, longevity and the Winograd-Cort explains. “We adopted a one-hour-long for- level of community involvement they were able to achieve,” mat and chose presentation topics not only because they are says Yale SEA chapter President Elizabeth Winograd- interesting but because of surrounding controversy, misun- Cort. “These are our goals as well, and we had been looking derstanding and lawmaking activity. We want our audiences for an effective way to communicate important and often to be better informed in order to make a difference them- controversial scientific breakthroughs to the New Haven selves, either by writing to their representatives, by voting or community.” by raising community consciousness.” The Yale students took the SITN concept and ran with it, Already, participants say, the Yale version of SITN has had she says. a measurable impact.

8 steps to starting your own Science in the News program 1. Recruit volunteers: You need a core group of dedicated, enthusiastic people with scientific expertise, plus a few contributing volunteers to staff specific efforts. 2. Focus: Start by choosing a single event you want to host or participate in that serves an unfulfilled need in your community. Expand from there, and don’t be afraid to try more than once. 3. Know your audience: Design programs with a particular audience in mind. This will improve the quality and reception of the event as well as the effectiveness of advertising. 4. Secure funding: Programs like SITN do not require a lot of funding. Be creative: Ask for donations and apply for public service grants. 5. Advertise: Choose advertising strategies with your audience in mind, and capitalize on joint advertising with other groups or events. Collect data to guide future advertising decisions. 6. Quality control: Determining how to evaluate, maintain and enhance program quality is the secret to long-term success. Ask for details on SITN’s quality- control measures and the Science Presentation as a Performing Art course. 7. Collect data: Design surveys and other metrics to gauge the impact and effectiveness of your programs. This will spur continued development in Steps 1 – 6. As you establish your program, don’t forget to keep track of your volunteer alumni as well. Throughout the opening Carnival Day of the 2009 Cambridge Science Festival, an all-ages audience filed by and stood in line to 8. Contact SITN: SITN has more than a decade of meet and greet a “zoo” of the major invertebrate model research experience implementing public outreach programs organisms — including bacterial biofilms, plants, yeast, slime and is happy to share successes, failures and insider mold, worms, fruit flies, zebrafish larvae and mammalian cells — tips. Start the conversation by emailing sitnboston@ and their scientist “zoo handlers” at the Science in the News gmail.com. Model Organism Zoo.

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“We’ve been invited to speak to New Haven high school students in summer programs and during the school year Communicating science this fall,” Winograd-Cort says, “and we are dedicated to keep- Communicating science is a top priority for the ASBMB ing our program running for years to come.” Public Affairs Advisory Committee. By working with Winograd-Cort insists that collaboration between the Yale Science in the News, the PAAC recognizes graduate and Harvard groups ensured success of the fledgling program: students’ energy and passion for communicating science “Harvard’s SITN program gave us all kinds of support, from and aims to engage growing numbers of participants outlining where they spend their money to giving us funds to across the country — scientists and nonscientists — to obtain and distribute advertising postcards. Ultimately, it was talk about science and to enhance the public’s percep- the knowledge that something like SITN existed that made us tions of scientists and the importance of our work. PAAC believe we could pull off such an undertaking.” will continue to identify and explore effective science- To read more about SITN and find out how you might communication programs and initiatives, examples of start an outreach program in your own community, visit which will be reported in future ASBMB Today features http://sitn.hms.harvard.edu. or in the SciComm section. In addition, an ASBMB sym- posium at the 2012 Experimental Biology meeting in San Morgan Thompson ([email protected]) Diego will highlight science communication. We welcome is a graduate student at Harvard Medical School your feedback on science communications issues at and served as co-director of Science in the News [email protected]. —Lee Gehrke for two years beginning in January 2008.

2012 ASBMB ANNUAL MEETING

GENE REGULATION DNA REPLICATION, RECOMBINATION, REPAIR

RNA PROTEIN SYNTHESIS & TARGETING

CHEMICAL BIOLOGY AND BIOCATALYSIS DRUG DEVELOPMENT

SYSTEMS BIOLOGY LIPID and LIPID SIGNALING

METABOLISM and DISEASE ORGANELLE DYNAMICS

GLYCOBIOLOGY

Travel Awards & Abstract Submission Deadline: Nov. 8 April 21–25, 2012 www.asbmb.org/meetings San Diego, CA

HalfPageHorizontal.indd 1 8/9/2011 2:29:41 PM

September 2011 ASBMB Today 19 featurestory Experimentation from hundreds of miles away Remote data acquisition offers some researchers access to instruments usually out of their reach BY JIANFEI (JEFFREY) ZHAO

icture this: You’re in your pajamas, sitting in front of a Pcomputer. After a cup of coffee, you turn on the com- puter, log in to a secure website, start your favorite instrument remotely and begin to collect data. You then turn your atten- tion to analyzing the data you acquired and downloaded from preliminary data using a local X-ray diffractometer, Yin relies your earlier experiments. Occasionally, you check the progress on the Advanced Photon Source, a synchrotron facility at of your experiment and modify some of the instrument param- the Argonne National Laboratory, to refine the structure at a eters accordingly. And voilà, several hours later, the new data higher resolution. are ready for your next round of analysis. She describes the synchrotron as a giant ring where elec- Is this a dream? Science fiction? Admittedly, for most bio- trons are accelerated to near light-speed to produce high- medical researchers, it is not yet reality, but for some privileged energy X-ray beams. With a nearly $1 billion construction scientists, especially structural biologists, the remote access of cost and an 80-acre footprint, it would be impossible for most rare and expensive instruments is both a reality and a necessity. academic institutions to build a synchrotron. Indeed, by the latest count from lightsource.org, a high-energy light source Remote X-ray crystallography facility advocacy group, only five synchrotron facilities in the “You need an X-ray source with high intensity to solve the U.S. have the capability to solve the structures of proteins with three-dimensional structures of large macrobiomolecular imperfect crystallization that Yin creates. complexes at angstrom resolution,” explains Roy Mariuzza, a However, using NoMachine, a commercially available desk- professor of cell biology and molecular genetics at the Institute top virtualization and remote-access management program, for Bioscience and Biotechnology Research at the University in combination with JBluice-EPICS, the beamline control of Maryland, College Park. “The X-ray source we need is only software developed by APS and the Stanford Synchrotron available in a few national labs in the U.S.” Radiation Lightsource, Yin can control the X-ray beamline — Although in-house X-ray crystallography equipment is a section of the synchrotron — and collect data through a ubiquitous, it cannot generate X-rays with intensity high secure network at her lab in Maryland without the hassle and enough for the Mariuzza group’s research. “The molecular cost of traveling. “The software is very user-friendly,” says Yin. packing of the crystals of my protein complexes is often defec- After initially being supervised by a colleague who is an expe- tive to various degrees,” says Yiyuan Yin, who recently gradu- rienced APS user, Yin was approved to independently operate ated from the Mariuzza lab. the machine remotely. Yin wants to understand the interactions between CD4, Nagarajan Venugopalan, a crystallographer at the APS, says MHC II and the T-cell receptor — three proteins involved that, to schedule beamline time, Yin had to submit a proposal in multiple sclerosis — by solving the crystal structure of that was evaluated for scientific merit. After the proposal was a CD4-MHC II-T-cell receptor complex. After producing approved, Yin was given a specific time during which she could

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use the synchrotron. The usage of the beamline is free for users Weibin Chen, principal chemist of the Biopharmaceutical who are funded by the National Institutes of Health. Sciences group at Waters, says that remote access allows scien- When the appointment approaches, Yin packs her crystals tists at Waters to change parameters, such as solution gradients, in a specially designed rack that can be handled by a robot of mass spectrometers and even to reset the instruments. When system at the APS and ships the rack in a liquid nitrogen tank Chen, like most Bostonians, was kept at home by the heavy to Argonne. As Yin’s host scientist, Venugopalan loads the snowfall this past winter, he was able to control his mass spec- crystals onto the beamline machine. From there, Yin takes trometer remotely and conduct his planned experiments. over the machine through JBluice-EPICS and usually runs For the David H. Murdock Research Institute in Kannapo- three continuous eight-hour sessions. “Running the marathon lis, N.C., the desire to offer remote access to some of its state- experiments in the familiar setting of our own lab reduces a lot of-the-art instruments arises from its vision for collaboration. of stress,” says Yin. Mike Luther, president of the DHMRI, says that the institute During the experiment, Venugopalan is on call to assist supports research and development projects with partners who Yin with any technical questions. He also provides scientific are located both on and off campus. The cost of each project is advice for data analysis and develops new X-ray technologies decided on a case-by-case basis. to help beamline users. Venugopalan explains that the beam- Zhong Wang of the Bio-Imaging Facility at Hunter College, lines undergo constant improvements. “We are in the planning City University of New York, wants external users to share the phase of upgrading one of our beamlines to achieve a 1-micron facility’s high-end microscopes, because smaller universities X-ray beam size,” he says. “It will help in achieving diffraction “may not have enough funding to support expensive instru- from extremely small crystals and also help in the reduction of ments.” Wang says that outside researchers can remotely access radiation damage to the crystals.” the confocal microscopes equipped with WebEx and a video- conferencing system. Remote microscopy For a few lucky scientists working with Sriram Subramaniam, The future of remote a senior investigator at the National Cancer Institute, remote The remote access of sophisticated instruments, except in the access to electron microscopes from home and around the case of synchrotron facilities, largely remains off limits for clock is becoming the norm. With Virtual Network Comput- academic researchers. Some instrumentation experts speculate ing, a desktop-sharing system, researchers in Subramaniam’s that the low availability partly is due to the complexities of the group can remotely control the workstation that physically operations. “Each lab member undergoes months of intense connects with the microscope and see the exact same screen training before he or she can operate the electron microscope that pops up on the microscope’s workstation. Joel Meyerson, independently or remotely,” notes graduate student Meyerson. a graduate student working in the Subramaniam lab, says that However, there is a growing need for remote access, as the remote control provides flexibility to the lab members, sophisticated instruments are “starting to cost more both in especially to scientists who have young children. terms of purchase and maintenance,” says Tobias Starborg, senior experimental officer of the electron microscope facility Remote servicing at the University of Manchester. He adds that “the only way For Bruker Daltonics and Waters, two analytical instrumen- new techniques get developed [by the facilities is to have] a tation providers, remote access means cost efficiency and constant flow of users wanting to try different things.” uninterrupted workflow. Doug Boyd, a sales representative Remote control of instruments could be a double-edged at Bruker Daltonics, explains that Bruker service engineers sword, however. Chen predicts that remote control via smart- use WebEx, a commercial software package similar to Virtual phone will be the next step. “[But] would I really like to control Network Computing and NoMachine, to diagnose their instru- the mass spectrometer on the beach?” asks Chen with a smile. ments remotely and help customers troubleshoot. “The engi- neers may detect a faulty part, order a replacement and even remotely teach the customer to install the part, which could Jianfei (Jeffrey) Zhao ([email protected]) is potentially save the customer hundreds of dollars or more,” he a postdoctoral fellow at the National Cancer says, adding that remote work also saves time because many Institute. inquiries are “resolved without the need for parts or an onsite service visit.”

September 2011 ASBMB Today 21 featurestory Celebrating postdocs They do the heavy lifting all year long in labs across the globe. The third week of this month is dedicated to showing our appreciation. BY ROBERT BARRETT AND KATE M. SLEETH

National Postdoctoral Awareness Week runs from Sept. 19 through Sept. 23. Initiated by the National Postdoctoral Association in 2009, the observance is intended to highlight the contributions that postdoctoral scholars make to science and to spur institutions to show their appreciation in various ways. Here, Robert Barrett and Kate M. Sleeth of the National Postdoctoral Association explain how the observance came to be and how their organization can serve the postdocs that labs rely on every day.

ational Postdoctoral Awareness Week initially began U.S., and the training has become the natural next career step N as a one-day event known as National Postdoc Appre- for newly minted Ph.D.s. The temporary period of mentored ciation Day, which was held Sept. 24, 2009. The inaugural research or scholarly training allows them to acquire the skills observance was a great success, with more than 50 institu- needed to pursue independent careers. tions in the United States and others as far away as Australia In earlier years, there was no limit to how many years one participating. could remain in a postdoctoral position, but new rules for The one-day celebration subsequently was expanded to a National Institutes of Health grant eligibility have capped the full week in September to allow institutions greater flexibility. experience at five years for many institutions. In 2010, more than 110 events were held in 30 U.S. states. Postdoctoral scholars are responsible for the majority of research output in the United States and drive the entire What happens during the observance research enterprise in both academic and industrial settings. The events that are held vary widely depending on the needs In 2008, the National Science Foundation’s Science and Engi- and resources of the participating institutions. Some host neering Indicators report estimated that there were about 89,000 symposia that allow postdocs to showcase their current postdoctoral scholars involved in research in the United States. projects. Others invite noted speakers to give lectures. Still oth- In addition, although postdoctoral scholars often work up to 80 ers provide seminars on grant writing and careers outside of hours a week, they earn an average of only $38,000 a year. academia. Seminars also are used to showcase the latest tech- Postdocs are motivated by their passion for discovery and nology available for use by postdocs. Almost all institutions the scientific method and their wish to make a positive dif- support networking events with free food and drinks. ference in the world. To fulfill these desires, many sacrifice financial security and often work in countries far from their Why postdocs deserve recognition families. The NPA initiated the observance so that institutions col- lectively could recognize the value of postdocs to campuses, The National Postdoctoral Association facilities and the scientific enterprise in general. The primary aim of the association is to advance the U.S. The number of postdocs has been increasing steadily in the research enterprise by maximizing the effectiveness of the

22 ASBMB Today September 2011 featurestory

research community and enhancing the quality of the postdoc- Offices also have been opened by institutions that have strong toral experience for all participants. The nonprofit was founded Associations, which lobby the administration and communicate in 2003 by seven members at institutions throughout the U.S. how important postdoctoral training and support are. Now headquartered in Washington, D.C., the NPA serves Even if your institution’s association has limited funds or more than 1,500 members and more than 180 institutions that none at all, it is still possible to organize a postdoc aware- employ 40,000-plus postdoctoral scholars. ness week event. For example, you can coordinate something Throughout the years, the NPA continually has advocated as simple as a coffee hour in a local café or a happy hour at a for better conditions for postdocs, playing a prominent role bar or restaurant at which everyone purchases his or her own in how the NIH and NSF have defined the position; advocat- food and beverages. If your city or region is home to multiple ing for the NIH Pathways to Independence award, which research institutions, consider pooling resources and having substantially helps postdocs transition to tenure-track faculty one large event. positions; and asking the NIH and NSF to expand their data collection regarding postdocs supported by research grants and Robert Barrett (Robert.Barrett@ to ensure that postdocs are properly mentored and trained. In cshs.org) is a postdoctoral scholar September 2010, the awareness week was recognized by the in the Inflammatory Bowel & U.S. House of Representatives. Immunobiology Research Institute in Cedars Sinai Medical Center, Building a support network and Kate M. Sleeth ([email protected]) is a postdoctoral fellow in the department of immunology at the Beckman Research The NPA also offers assistance and advice on how to form Institute at the City of Hope. postdoctoral associations and postdoctoral offices at institu- tions. Associations are generally run by postdocs, and offices are generally run by academic faculty directors or nonfaculty directors or coordinators. Yet the aim of both is the same: to Other ways to show your support improve the postdoctoral experience. Associations often wel- • Become a member of the National Postdoctoral Association. come volunteers who wish to capitalize on related networking Visit www.nationalpostdoc.org. opportunities. • Purchase an item from the NPA store. There are items for every budget, including clothing, greeting cards, mugs, If you are a postdoc and are unsure if your institution has notebooks, bags and calendars — all with logos and fun either an association or an office, check with your graduate slogans on them. Visit www.nationalpostdoc.org/store- program leadership or your institution’s human resources office. merchandise. If there is no association on campus, combine forces with other • Participate in an awareness week event. Visit www.national dedicated and enthusiastic people and start one. Lots of associa- postdoc.org/meetings-and-events/appreciation. tions across America have started as grassroots efforts. reminder:onlinegraduationsurvey The deadline for the 2010-2011 ASBMB Thank you, James K. Zimmerman Graduation Survey is Sept. 30. Peter Kennelly, If your department/program offers a Education and Professional Development Committee degree in biochemistry and/or molecular Squire Booker, biology, chemistry with a biochemistry Minority Affairs Committee track, or biotechnology, please check with Takita Sumter, Minority Affairs Committee your unit chair/head to see if a response Benjamin D. Caldwell, has been sent. Undergraduate Affiliate Network featurestory Studying science. Serving others. Course puts biochemistry students in real-world situations, teaching lessons they won’t find in textbooks or the lab. BY JONATHAN DATTELBAUM

Building the course When students enroll in Jonathan Dattelbaum’s biochemistry course at the University of Richmond, they expect to learn The process for developing a community-based learning about the basics of the field. But Dattelbaum’s course is about experience began as part of a biochemistry laboratory section the unexpected, and that’s on purpose. Community-based I was teaching as a first-year faculty member. The goal was to provide a complementary learning experience for students learning extends the learning experience for students outside and not to replace specific laboratory material. the classroom through interactions with the public. Here, Dat- This teaching module was developed in consultation with telbaum, an associate professor of chemistry and co-director the Bonner Center for Civic Engagement at the University of the Biochemistry and Molecular Biology Interdisciplinary of Richmond. I wanted to challenge the biochemistry lab Program at the University of Richmond, reflects on how send- students to take part in community-based service where ing students out into the world has proved to be a valuable biochemistry plays a role. The pilot project asked students teaching pedagogy. to complete at least three hours of service in the Richmond community at one of four selected organizations: the Ameri- ommunity-based learning experiences take many can Lung Association of Virginia, the CrossOver Clinic, the Cforms, including bringing in speakers from the com- March of Dimes’ Central Virginia Division and the National munity, producing documentaries, teaching course materials Kidney Foundation of the Virginias. While the students participated in a variety of activities in primary and secondary schools, or conducting field work. depending on the needs of the organizations, the connecting I chose service learning, because it provides an excellent force was the interaction students had with clients at each umbrella for student exploration of the connections between site, allowing for personal observations of diseases, condi- textbook concepts and real-world applications, particularly tions and situations. for medical and biotechnological fields. For their efforts, students received the equivalent of one Many science faculty members believe that science is problem set toward the laboratory grade in the course. To learned by doing. Refining what it means to be actively assess this activity, I designed a report sheet that asked each engaged in teaching science is important for our students as student to provide a short paragraph describing his or her they move through the curriculum and into the workforce. experience and to reflect on how biochemistry was involved. In the sciences, one of the most common formats for This lab module became a pilot project that ran for three active teaching is the lab-based science class, in which semesters. students learn important hands-on skills and applications. More recently, many schools have invested in undergraduate Evolution of the course research programs that enhance experiential collaborations I later expanded the community-based learning experience between students and faculty. While learning laboratory into the lecture component to show students how the course skills is an important part of science education, many sci- material relates to society. The number of topics covered in ence majors will not become research laboratory scientists. I lecture is greater, which allows the inclusion of more com- believe that finding ways to develop life skills, such as study- munity organizations in the program. In the end, more than ing the application of science in society, learning more about 40 students participated per year in the CBL project. community and working with different population sectors, My students chose from selected sites in the Richmond requires creating learning opportunities outside of traditional community and worked for a minimum of 15 hours. While laboratory-based courses. the selected sites were preferred because of the network of

24 ASBMB Today September 2011 featurestory

contacts I developed at them, students were allowed to work at different locations with prior approval. They also were required to keep well- written blog journals summarizing their activi- ties within 24 hours of each visit. Here’s one excerpt from an entry: “I have come to learn that some days are better than others in the nursing home, both for the patients and the staff. The patient I visit was con- gested and had to get a chest X-ray but turned out to be fine and returned to the nursing home the next day. Since, she has been much less talkative (compared to the minimal amount she did). It is hard assessing how someone is doing/feeling when you can’t really communicate with them, and incredibly frustrating on both ends, whether patient or nurse.” And here’s another: “I am TB negative! My skin test had a bump University of Richmond student Heather Hollis’s community-based learning site that was 1mm off of unacceptable size for being in was the Fan Free Clinic in Richmond, Va. a hospital setting. They injected me with tubercu- losis antigen, (and) the size of my inflammatory response is dictated by the amount of TB antibodies I have. A Assessing impact person who has been exposed to TB in the past (and thus has Student evaluations consistently showed that about two- a large AB count) will have a larger inflammatory response, thirds of students were serving in the community for the hence a larger bump. If I had failed the size test, they would first time and that many students worked more hours than then have taken an X-ray to check for nodules in my lungs.” the course required. About two-thirds also said that they learned more in the course because of the community- Student reflections and evaluations based project. At the end of the term, each student wrote a literature-based paper with a reflective component focused on some bio- chemical aspect related to the mission of his or her work site receptors, was administered, and a violent reaction ensued, and experiences working with individuals there. suggesting heroin overdose. The student presented this The students also completed an evaluation form that pro- example in the context of a recent lecture on protein-ligand vided some quantitative feedback. After the first year of this binding. Additionally, the age of the patient helped students project, the most important critique I received was that the see the significance of the concept of small-molecule binding service hours felt like extra work that was not really a part of and affinity, which is a difficult topic for some students. the course. I, therefore, turned my attention to integrating A second student working at a local facility to transition the experience throughout the entire semester. I did this by drug addicts back into society observed the detoxification explaining on the first day of class why I thought this project process and connected this with some of what we know about has value for learning biochemistry. the biochemical processes in the brain that favor addiction Additionally, I used class time every other week to let and bring about pain during withdrawal. Additionally, she students present information about their experiences and went even further to describe the socioeconomic diversity explain how those experiences related to biochemistry. present in the facility, which was something this student had For example, a student who volunteered with a local res- not expected to find. cue squad described the treatment of a 19-year-old girl expe- The student presentations provided the most significant riencing a possible sleeping pill or heroin overdose. Narcan, change in student attitudes toward the project. The number a potent narcotic antagonist that works by blocking opiate of students reporting that they were able to see how bio-

September 2011 ASBMB Today 25 featurestory continued

Biochemistry students, from left, Caroline O’Rourke, Tran Doan and Miles Johnson participated in the community-based learning module established by University of Richmond associate professor Jonathan Dattelbaum.

By THe NUMBeRS municated to students in advance. Developing relation- Fall 2008 24 students ships with volunteer coordinators is invaluable for finding projects that align well with course objectives. However, Spring 2009 21 students such organizations have high turnover and require con- Fall 2009 15 students stant re-evaluation. This extra time is an important factor to consider at the onset. Spring 2010 26 students There is also a risk that not all students will be inter- TOTAl STUDeNTS 86 students ested in participating for any number of reasons, and issues are likely to arise, including problems with transpor- x 15 hours = tation, with nonresponsive organizations and with extra TOTAL HOURS 1,290 hours time for the assignment. Student frustration comes out in course evaluations. If one has unsupportive departmental or administrative colleagues, this may be a particular con- chemistry subject material related to society rose from 67 cern for untenured faculty. percent in the first year to 92 percent in the second year. As a result of bringing the student presentations into the A teacher’s reflections lecture, the learning was no longer isolated to individual Over the four semesters that I taught this community-based students who went out into the Richmond community learning course, my students contributed more than 1,290 alone and wrote term papers that only I read. This became hours of service to the Richmond community. As research a powerful mechanism to share learning experiences in scientists, we can have a very positive impact on the train- the classroom, where connections could be illustrated by ing of a small number of laboratory students, but, as teachers students and not just by me. providing opportunities like this one, there can be a multiplier effect in that our students take ownership of their learning to Considerations enhance the community in a meaningful way. There are a few barriers to making the most of community- based learning experiences. Jonathan Dattelbaum ([email protected]) One important factor to consider is that, as the course is an associate professor of chemistry and instructor, you must give up a certain level of control over co-director of the Biochemistry and Molecular the amount of learning that occurs at the sites. Some will Biology Interdisciplinary Program at the be better than others, and that must be accepted and com- University of Richmond.

26 ASBMB Today September 2011 featurestory Inquiry-based learning in K – 12 BY MARGARET JOHNSON

aving received clear and inspiring directives for imple- One answer is that students don’t need lots of classroom H menting change in the way we teach undergraduates time or resources to ask questions that reflect an innate science, we now can focus on mechanisms to initiate that need to know or natural curiosity. Later, in college, they change in instruction at an earlier stage in the education can learn how to formulate scientific questions and utilize process. For the purpose of this article, we consider the scientific tools. Nature already has performed many of the science-education process as having two critical phases: an experiments that can be used in K – 12. In addition, nearby initial phase of inquiry-based learning (K – 12 science) and a research institutions can help train K – 12 teachers using maturation phase of inquiry-based learning (undergraduate faculty-based research. Thus, the teacher needs only to learn science education and beyond). how to use nature’s experiments to get the students to ask As you would suspect, it is much more difficult to initiate questions — questions such as “How do we know?” inquiry-based learning at the maturation phase than at the Once students understand that scientific information is initiation phase. The question, then, is: What we can do to based on evidence and that they have the right to ask for induce inquiry-based instruction at the initial phase so that that evidence, then they are ready to understand the scien- students enter undergraduate courses in the questioning tific process. mode rather than the passive-recipient-of-information mode? Here’s hoping that resource or time limits inspire numer- Having students who enter college in the questioning mode ous creative ways for K – 12 teachers to initiate inquiry- will allow college science instructors to implement immedi- based learning so that students enter undergraduate science ately the exciting changes a national conference organized by courses in the questioning mode. the American Association for the Advancement of Science and supported by the National Science Foundation recom- mended for improving undergraduate science education. Margaret Johnson ([email protected]. So how can the K – 12 science teacher initiate the edu) is an associate professor at the University inquiry-based learning phase when there is little classroom of Alabama. time left to teach science and no resources to purchase sci- ence teaching materials?

A few ideas point for inquiry-based instruction. If I’m working on something without saying what I’m doing, then Methods to induce inquiry-based learning at the K – 12 level: students will ask the following questions: Use newspaper and Internet articles about What is that? Why are you doing that? current hot topics in How does that work? Who made that? science and research to Perform an experiment to engage start discussion. Stem-cell students in discussion. For instance, research is a favorite. Questions use your imagination to generate questions using only foil, give the teacher the opportunity a magnifying glass and soil from outside your building. After to incorporate biological the first round of observations and principles into the questions, pour water on the soil. discussion. Take advantage of a natural Invite local researchers to lead experiment. Bring agricultural and demonstrations. A real plus in doing other natural resources to the this is that the scientist can bring portable classroom. Different colored equipment. The equipment should not be vegetables (of the same kind) used for show and tell but as a starting or flowers are real winners.

September 2011 ASBMB Today 27 featurestory Biotic games Play with living organisms BY NANCY VAN PROOYEN

t’s easy to imagine how computer games greatly improve I verbal and mathematical proficiency, but can they be used to foster an interest in science? Stanford University’s Ingmar Riedel-Kruse is convinced they can. An assistant professor of bioengineering, Riedel-Kruse and his lab group have developed the first biotic games, which involve manipulating biological processes in real time. They be prompted to change directions, but they move in a random use various visualization techniques to illustrate and moni- path, which makes the games challenging. tor these processes on a computer screen with a gamelike In a game inspired by the classic arcade game Pac-Man, interface. which Riedel-Kruse’s team has dubbed PAC-mecium, paramecia The inspiration to create biotic games came from reading are placed in a square fluid chamber that has electrodes along about the history of computers and video games, Riedel- each side. The player controls the swarm by applying electric Kruse explained. fields along two axes with a hand-held controller. The motion “Computer development enabled video games. Since of the paramecia is captured with a webcam and displayed on a biotechnology is currently undergoing a similar revolution, computer screen. Points are scored by directing the paramecia it struck me that biotechnology could also be a medium for a to gobble up virtual yeast food shown on the computer screen. new type of game,” he said. However, players have to help the paramecia avoid hungry vir- Many video games attempt to mimic real life, but biotic tual zebrafish larvae that move across the screen. games use actual life forms, such as paramecia and yeast. The second class of games involves risk and logic. - Players learn about a variety of biological, chemical and Race is inspired by horse racing, in which gamblers make bets physical properties without dealing with the rigors of formal on the order that horse-jockey pairings will reach the finish line. experiments. Additionally, living organisms often respond in In the biotic version, the horse-jockey pairs are small DNA oligo- random ways, which makes them fascinating to watch. nucleotides, or primers, that bind with a range of affinities to “Biotic games enable interesting play experiences based on DNA during a polymerase chain reaction, a common molecular real-life phenomena, biological unpredictability or the stimu- technique used to replicate DNA sequences. lation of olfactory senses,” Riedel-Kruse said. “We hope that, Players watch in real time the amplification of DNA and with by playing games involving biology of a scale too small to see each cycle obtain new information about the order and reaction with the naked eye, people will realize how amazing these efficiencies of the primer pairs. In each subsequent cycle, players processes are, and they’ll get curious and want to know more.” make more bets; thus, the strategy is to balance risky, limited- Riedel-Kruse designed three types of games inspired information bets with secure, logic-driven bets. by classic video games. The results of the design efforts are The final class of games involves the use of olfactory senses. reported in the 10th-anniversary issue of Lab on a Chip, pub- Prisoner’s Smellemma is based on the classic problem in game lished by the Royal Society of Chemistry. theory known as the Prisoner’s Dilemma, which demonstrates The first set of games uses single-celled organisms that lack that people may not always cooperate even if it is in their best brains and the capacity to feel pain. Higher-level organisms interests. Prisoner’s Smellemma is played with yeast, which emit are not being used, Riedel-Kruse emphasizes, as “safety and a vinegarlike smell similar to that of freshly baked bread. Each bioethical issues were considered in the design of the games.” player receives a yeast strain and buffer. Players mix either buffer One organism of choice was the paramecium, which is a or yeast strain with their opponent’s, smell the mixture and guess ciliated single-celled organism that swims in a run-and-tum- what the other player did. Players score points by guessing cor- ble motion and can be directed to move in a guided direction rectly whether their opponent is cooperating or opposing them. through both electrical and chemical signals. Paramecia can These biotic games mark a milestone in the computer gaming

28 ASBMB Today September 2011 featurestory

world. It’s the first time a game has been created in which the player’s actions influence living organisms in real time. It’s easy examples of scientific to see how these games can be used for educational purposes, crowdsourcing for fun Riedel-Kruse said, especially in the classroom to get students Other scientists have designed Internet-based video excited about biology. games to utilize the collective power of many people “Many computer experts discovered their love for computers working on one problem. In the gaming world, this is when playing games,” he said. “Biotic games could have the same referred to as crowdsourcing or citizen science, in which inspiring effect for biology and biotechnology.” a task is delegated to a group of individuals with one Riedel-Kruse said he also is optimistic that these games will common goal. inspire the public to contribute to biomedical research, because Vijay Pande at Stanford University created a protein- games can be used by small armies of players or researchers who folding game (folding@home) that is run on the world’s run experiments and gather data as they play. largest supercomputer to generate new ideas about “Ideally we would like to structure a game so that many how proteins fold. people will play, and each person feels like they are making a In addition, EteRNA, a ribonucleic acid folding game, valuable contribution,” he said. “The more people thinking about allows the public to create new RNA molecular struc- a common problem with different backgrounds, the more likely tures. The players are scored based on known chemical we are able to solve that problem.” properties of the RNA structure. The highest-scoring RNA molecules are tested in the laboratory. EteRNA Nancy Van Prooyen ([email protected]) was developed as a collaboration between the Carnegie is a postdoctoral fellow at the University of Mellon University and the Bio-X.Game Center, an inter- California, San Francisco. disciplinary research center at Stanford University. lipid news A report from the ASBMB Lipid Division. electrophilic fatty acids: redox-derived signaling mediators BY STEVEN R. WOODCOCK AND BRUCE A. FREEMAN

ecent advances from a variety of labora- R tories reveal that free radical-induced lipid oxidation products can mediate potent anti- inflammatory and beneficial metabolic reac- tions. Fatty acids, at first glance, are among the simplest of biological molecules: straight chain hydrocarbons with a single polar terminus and at most a few cis-double bonds in either a methylene-skipped or conjugated diene pattern. In poly- tively, the hydroxyl may be directly oxidized via enzymatic unsaturated fatty acids, the low-bond dissociation energy or nonenzymatic pathways to an aldehyde or ketone. The of the doubly allylic methylene renders them α,β-unsaturated carbonyl, now conjugated to the diene, relatively reactive. Fatty acid ligation to proteins is typically forms a powerful electron-withdrawing group. This moiety accomplished by the formation of esters or thioesters, is labile to reaction with available nucleophiles, such as which increases lipophilicity, can modify protein function protein thiol or histidine residues. Similarly, NO-derived and alters the anatomic distribution of modified proteins. reactive species can instead nitrate the fatty acid by nitro- In the context of cell signaling, the stereospecific oxy- gen dioxide-mediated free radical addition mechanisms. genation of not only arachidonic acid but also other poly- The resulting nitro-fatty acids are even more electron- unsaturated fatty acids can be catalyzed by the heme and deficient and thus are a strongly electrophilic and kinetically nonheme iron-containing proteins cyclooxygenase-1 and -2 reactive species. The resulting oxidized or nitrated fatty as well as 5-, 12- and 12/15-lipoxygenases. These products acids, whether free or esterified, exhibit distinct structural are typically viewed as ligands for specific G-protein-coupled and biochemical properties and can modulate the activity receptors that propagate inflammatory responses. Notably, of multiple cell signaling pathways. by virtue of their reactive dienes, fatty acids also are suscep- The electrophilic reactivity of both α,β-unsaturated tible to more random oxidation by the adventitious oxidants carbonyl- and nitro-fatty acid derivatives is the basis for their produced during mitochondrial respiration, environmental signaling capacity. Double bonds conjugated to a strong oxidants, and the inflammatory activation of cellular nitric electron withdrawing group are susceptible to Michael .- oxide (NO) synthase and superoxide (O2 ) and addition. This is the reversible addition of a nucleophile to peroxide (H2O2)-generating NAD(P)H oxidase activities. the electrophile, accompanied by bond-rearrangement and These reactive species are not exclusively toxic, because proton transfer, to yield adducted (or alkylated) products. recent advances show they also can serve as salutary In the decidedly reducing cytosolic milieu, most biological signaling mediators by virtue of an ability to confer post- functional groups are electron rich, and some are potentially translational protein modifications. nucleophilic. This redox balance is maintained by gluta- Polyunsaturated fatty acids are easily oxidized to hydro- thione, which is a prevalent nucleophile as well as antioxi- peroxyl and hydroxyl derivatives, with multiple enzymatic dant. The adduction of electrophilic fatty acids to thiol- or mechanisms having evolved to further metabolize these amine-containing proteins via Michael addition introduces a intermediates. In the process of oxidation, double-bond post-translational modification of proteins, conferring altered rearrangments occur, such as from cis- to trans- and into cellular distribution, conformation and catalytic activity. conjugation with a neighboring double bond. This latter It is the combination of electrophilic adduction with the species is potentially reactive via the electron-rich conju- reversibility of this reaction that may be the most important gated diene and may be subject to further modification by aspect of this reactivity of soft electrophiles (figure). An irre- electron-deficient or unpaired reactive species. Alterna- versible reaction is essentially toxic, while a reversible modi-

30 ASBMB Today September 2011 lipid news

fication conversely is a typical event; molecules are modified detected in both animal models and clinically (1, 2). and remodified in continuous succession throughout the cell Why are electrophilic fatty acids relevant in biology? as a normal aspect of metabolism. Multiple transcriptional regulation events and nuclear lipid Detection of these fatty-acid products must consider receptors such as PPARγ are potently modulated by these their small proportion among free fatty acids while also species, resulting in predominantly anti-inflammatory and accounting for the bioavailable pools that already are beneficial gene expression and metabolic responses (3). adducted to proteins. The reversible electrophilicity of these One can envision that the redox-dependent generation of molecules has been exploited as an analytical methodol- electrophilic lipid products thus links gene expression to ogy designed to take advantage of their intrinsic properties. the metabolic and inflammatory status of tissues. To distinguish electron-rich fatty acids from oxidized or nitrated electrophilic species, simple methods for expos- Steven R. Woodcock (srw22@pitt. ing the analyte to competing thiol-containing nucleophiles edu) is an instructor and Bruce A. have been developed. Then trans-alkylation to low molecu- Freeman ([email protected]) the Irwin lar weight or immobilized nucleophiles permits capture of Fridovich professor and chairman of and chemical electrophilic species that are either free or already adducted biology at the University of Pittsburgh School of Medicine. via Michael addition to GSH or nucleophilic amino acids of proteins. In this regard, β-mercaptoethanol serves as an REFERENCES 1. Groeger A. L., Cipollina, C., Cole, M. P., Woodcock, S. R., Bonacci, G., effective electrophile trapping agent. After chromatographi- Rudolph, T. K., et al. Cyclooxygenase-2 generates anti-inflammatory mediators cally separating β-mercaptoethanol-adducted electrophiles, from omega-3 fatty acids. (2010) Nat. Chem. Biol. 6, 433 – 441. these adducts can be identified and analyzed by loss- 2. Schopfer, F. J., Batthyany, C., Baker, P. R., Bonacci, G., Cole, M. P., Rudolph, V., et al. Detection and quantification of protein adduction by electrophilic fatty of-mass observations as they are cleaved under ionizing acids: mitochondrial generation of fatty acid nitroalkene derivatives. (2009) Free mass-spectrometric conditions. Through this methodology, Radic. Biol. Med. 46, 1250 – 1259. 3. Rudolph, T. K., Freeman, B. A. Transduction of redox signaling by electrophile- new nitrated and oxidized fatty acid species are being protein reactions. (2009) Science Signaling. 2 (90) re7. education and training Undergraduate programs in BMB What makes them distinct? What makes them complete? BY PETER J. KENNELLY

A campus tour expanded to acknowledge the addition; in others, it was An enthusiastic young undergraduate is leading a group not. Another popular option, especially among smaller col- of high school students and their parents on a tour of leges and universities, was to assign responsibility for the Generic State University. BMB major to a consortium of two or more departments As they walk across the quadrangle, the undergradu- that usually includes both chemistry and biology. ate confidently points out building after building as his audience inquires: Where is the psychology department Does heterogeneity matter? located? Is that the biology building? Where’s English? Do these various models affect the quality of BMB educa- Where’s biology? Where’s engineering? Where is the tion nationwide? Does adding two or three BMB courses department of molecular biology? to the basic chemistry or biology curriculum offer the “I don’t think we have one,” the undergraduate replies. same learning opportunities as an integrated BMB curricu- “Where do students go if they are interested in studying lum designed from the ground up? enzymes, lipid metabolism or gene regulation?” Some of these structures expose students to a diverse “I’m not sure. Some major in biology. You can major in community of BMB faculty members. Others, however, biochemistry through the chemistry department, but you make-do with one or two token biochemists or even some still have to take P-Chem …” part-time instructors. While many faculty members and instructors work- A heterogeneous array of program models ing as outliers within biology, chemistry or other depart- For the bulk of the 20th century, colleges and universities ments are remarkable educators, it is difficult to believe were organized on modular principles. Every subject area that programs trying to get by with limited personnel and taught was the responsibility of an autonomous academic resources can maintain consistently high levels of quality department possessing its own faculty, staff, unit leader as readily as dedicated units that award BMB top prior- and space. Large departments often merited their own ity and access to the physical and human infrastructure buildings, with the collateral benefit of enshrining their generally associated with an autonomous department. disciplines in bricks and mortar for generations to come. This is not to say that departmental structure somehow As new disciplines emerged — aeronautical engineer- guarantees quality instruction. ing, psychology, computer science — during the steady Heterogeneity lies in the definition of the degree itself. expansion of the 1950s, colleges and universities added While many schools award a Bachelor of Science in new departmental modules. Eventually, however, spiraling biochemistry and molecular biology, others award degrees fiscal constraints rendered expansion by addition increas- in biochemistry alone or molecular biology alone. How do ingly impractical, driving institutions to seek ways of they differ? Are the core concepts and expected com- covering new areas by rearranging or repurposing assets petencies associated with a B.S. in molecular biology or within the existing unit structure. As relative latecomers on biochemistry consistent across colleges and universities? the scene, biochemistry and molecular biology programs followed a variety of paradigms. Should we care? Many schools, especially the larger research universi- The American Society for Biochemistry and Molecu- ties, established classic autonomous departments. Other lar Biology Education and Professional Development colleges and universities elected to add BMB to the port- Committee is committed to advancing the quality of folio of existing departments, with biochemistry frequently our discipline. Undergraduate BMB programs allow for falling under the purview of the chemistry department and the imaginations of aspiring biochemists and molecular molecular biology under that of the department of biology. biologists to become either further inspired or to grow In some cases, the title of the department was stale. Students either lay a foundation of analytical

32 ASBMB Today September 2011 education and training

ferred suite of major instruments and require that libraries provide access to at least 14 journals recommended by the ACS Commit- tee on Professional Training. While we do not propose to be as pro- scriptive and detail oriented as ACS, there are several areas in which ASBMB would like to make its influence felt. Therefore, for a student to qualify for an ASBMB accredited degree, he or she must graduate from an English eligible program. Key elements of an eligible program should include: Math Chemistry • 400 or more hours of hands-on, experiential learning across science, technology, engineering and math disciplines, • access to extracurricular research opportunities such as undergraduate research or internships, Bi gy olo • professional-development opportunities for faculty members, • opportunities for students to develop written ry and oral communications skills, and Bioc mist he • three qualified faculty members. This last element is perhaps the most problematic to deal with. For many small schools, it may be difficult to identify three History full-time faculty members, or the equivalent, whose primary allegiance is to the BMB program. Many small programs are getting by with only one or two faculty members. Should they be penalized just because they are small — a metric that does not correspond with quality? On the other hand, setting stan- reasoning skills, quantitative analysis, chemical function- dards for the sole purpose of not leaving someone out is alities and structural principles that promote success in hardly an approach that can be expected to earn credibil- the workplace and graduate and professional schools or ity and respect or to promote aspirational change. simply get by through rote memorization and other tricks The EPD is interested in hearing your ideas about what of the trade. criteria should be used to identify programs that meet the So, yes, ASBMB has a stake in the institutions and expectations of the ASBMB community and why. Simply members who perform the vital task of preparing our next send an email to [email protected]. generation of scientific leaders. When it comes to the issue of program infrastructure, accreditation programs such as the one being developed Peter J. Kennelly ([email protected]) is a professor by ASBMB have proved successful in setting threshold and head of the department of biochemistry at standards for personnel, curriculum, etc. The American Virginia Polytechnic Institute and State University. Chemical Society, for example, specifies that an accred- He also is chairman of the ASBMB Education and ited department must have at least four dedicated faculty Professional Development Committee. A report members. The ACS also goes so far as to suggest a pre- from the Education and Professional Development Committee.

September 2011 ASBMB Today 33 journalnews More ASBMB journal highlights at www.asbmb.org.

been diagnosed with cardiovascular disease than those The JouRNal of without cardiovascular disease. lIpId ReSeaRch While the study had limitations (particularly patients’ concurrent aspirin use and their lifetime smoking habits), the publication appears to be the first to consider bilirubin New risk marker level as a potential risk marker in an FH population and proposes that long-term use of a statin can protect that for cardiovascular population from cardiovascular disease. disease? Mary L. Chang ([email protected]) is managing editor of the Journal of Lipid Research and coordinating journal manager of BY MARY L. CHANG Molecular and Cellular Proteomics. When red blood cells break down, so does hemoglobin. A byproduct of this breakdown, bilirubin, has been hypoth- esized to act as an antioxidant; some in vitro studies have The JouRNal of suggested that low-density lipoprotein can be protected BIologIcal cheMISTRy from breakdown by oxidation by bilirubin. This, along with the idea that bilirubin has anti-inflammatory properties, may explain why low concentrations of serum bilirubin are ‘capsules’ will help associated with a higher risk for cardiovascular disease. Pernette R.W. authors tell their de Sauvage Nolting and scientific stories colleagues at BY ANGELA HOPP the Academic Last month, the Journal of Biological Chemistry rolled out Medical Center a new feature aimed at providing readers with succinct of Amsterdam, snapshots of the latest papers being published and expla- the Netherlands, nations of how those papers significantly advance our investigate understanding of biological processes. Each regular paper in the article now will be accompanied by a “Capsule,” a very brief, “Serum bilirubin four-part synopsis written by manuscript authors and vet- levels in familial ted by JBC reviewing editors and associate editors. Each hypercholester- “Capsule” will explain the background, results, conclusion olemia: a new and significance of the paper. To find out more about JBC risk marker for “Capsules,” read Editor-in-Chief Marty Fedor’s editorial on cardiovascu- the journal homepage. lar disease?” whether a statin Angela Hopp ([email protected]) is a science writer and handles public relations for ASBMB. can change blood bilirubin levels in people with familial hypercholesterolemia, a genetic disorder characterized by high levels of cholesterol, especially LDL. They also investigated whether bilirubin level was a reli- able risk marker for cardiovascular disease. Male patients between 18 and 80 years old who had one copy of the hypercholesterolemia gene were given a daily oral dose of statin for two years and followed for the entirety of this cross-sectional study. The statin was shown to reduce total cholesterol, LDL and triglyceride levels while elevating high-density lipoprotein; but, more importantly, median bilirubin levels increased from baseline after treatment. This increase was more obvious in patients who had

34 ASBMB Today September 2011 journalnews More ASBMB journal highlights at www.asbmb.org.

The JouRNal of BIologIcal cheMISTRy

ASBMB ANNUAL MEETING April 21-25, 2012 2012 San Diego, CA Travel Awards ASBMB will award several travel awards and grants to assist first authors presenting abstracts at the ASBMB Annual Meeting from April 21-25 in San Diego. Only one application will be accepted per applicant. The application site opens this month. • Child-Care Grant New editorial • Graduate Minority Travel Award board website Funded through the FASEB MARC Program • Graduate or Postdoctoral Travel Award connects authors, • Undergraduate Affiliate Network (UAN) editors Outstanding Chapter Award BY SARAH CRESPI • Undergraduate Affiliate Network (UAN) The JBC launched last month a new edito- Travel Award rial board website that highlights the board’s For chapters to designate their chapter or breadth of expertise and its newly formed regional meeting travel award winners only affinity groups. The affinity groups reflect differ- • Undergraduate Faculty Travel Award ent areas of biological chemistry based on the Faculty applicants must be the first authors on journal’s table-of-contents sections. Organizing the abstracts associated with the travel award board membership and journal content accord- applications. Students submitting travel award ing to affinity groups is meant to help authors applications and/or participating in the poster and readers focus on areas of particular interest competition must submit unique abstracts on within the broader field of biological chemistry. which they are the first authors. The goal of the new editorial site is to make it • Undergraduate Student Competitive easier for authors to determine which board Travel Award members are most suitable for handling their manuscripts before beginning the submis- sion process. To this end, the new website Travel Award and enables searches by name, institution and Abstract Submission Deadline: Nov. 8 keyword. www.asbmb.org/meeting2012

Sarah Crespi ([email protected]) is the media and technology project manager for ASBMB.

September 2011 ASBMB Today 35 minorityaffairs ‘life will happen and sometimes presents unforeseen challenges’

iTani Parker Johnson, an assistant professor in the K College of Pharmacy at Xavier University of Louisiana, was featured recently on the ASBMB website. In her Q&A with ASBMB’s education and professional development manager, Weiyi Zhao, Johnson reveals how she has successfully navigated the ups and downs of her professional and personal lives by calling on the special people in her support network.

Read the interview at http://bit.ly/r57kdu.

university of Wisconsin- university of cincinnati Stevens point department of chemistry chemistry department or Biological Sciences FACULTY POSITION ASSOCIATE/FULL PROFESSOR POSITION IN BIOCHEMISTRY As part of an initiative to develop an interdisciplinary cluster of researchers, The University of Wisconsin-Stevens Point Chem- the Department of Biological Sciences and the Department of Chemistry in istry Department (www.uwsp.edu/chemistry) invites the McMicken College of Arts and Sciences seek to fill a faculty position at applications for a tenure-track position in biochem- the rank of Associate or Full Professor. istry at the assistant professor level. The appoint- For this particular hire, the candidate’s research should foster collabora- ment will begin in August 2012. Ph.D. in Chemistry, tions across chemistry and biology, as well as other disciplines, and address Biochemistry, or a related field is required: must be biological function or history. Themes of particular interest include chemi- completed by August 1, 2012. cal biology, molecular biology, “-omics” and single molecule bioanalysis. Candidates will teach courses in biochemistry and The candidate will have the opportunity to collaborate with a variety of general chemistry as needs require. Applicants must groups with research strengths in areas such as the evolution of biological show promise for excellence in teaching and will be processes, nucleic acid chemistry, behavior and neuroscience, nanotechnol- expected to develop a research program involving ogy, paleobiology, environmental genomics, sensors, and structural biology. undergraduates. The ideal candidate should be an established, active researcher with Send hard copies of curriculum vitae, a statement of a record of productive mentoring, consistent publication, and substan- teaching philosophy, plans for proposed research, tial extramural funding. Responsibilities will include interfacing with other undergraduate and graduate transcripts, and three researchers in the College, maintaining a vigorous, externally funded letters of recommendation to: Chair of Search research program, mentoring of graduate students as well as postdocs, Committee, Department of Chemistry, University of teaching at the undergraduate and graduate levels, and service to the Wisconsin-Stevens Point, Stevens Point, WI 54481. university community. Application materials may not be sent electronically. Applications must be submitted online at www.jobsatuc.com and reference Letters of recommendation must come directly the job posting #211UC0035. Applicants must attach the following to their from references. Screening will begin on October online application: a cover letter, a short (3-5 pages) statement of research 17, 2011, and will continue until the position is filled. interests, list of four selected publications, a curriculum vitae and contact information for four references. Review of completed applications will UWSP is an Affirmative Action/Equal Opportunity Employer. Women, minorities, Vietnam era veterans, disabled veterans, continue until the position is filled. and individuals with disabilities are encouraged to apply. The University of Cincinnati is an equal opportunity / affirmative action employer. Employment will require a criminal background check. Women, people of color, people with disabilities and veterans are encouraged to apply.

36 ASBMB Today September 2011 T ired of dancing around?

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Affymetrix-USB_ExoSAP-IT-HT_ASBMB-Ad.indd 1 3/30/11 9:36 AM 2013ASBMB SPECIAL SYMPOSIA CALL FOR PROPOSALS

with the American Society for Biochemistry and Molecular Biology to bring your Pacommunityrtner together! ASBMB Special Symposia provides you, as a specialized researcher, a unique opportunity to present cutting-edge science mixed with active networking opportunities in an intimate setting.

HoFormat:w WMajoritye’r oef talksDi selectedffere fnromt: abstracts, invited speakers, 2-4 days in length

Attendees: 75-200 attendees, including investigators, industry professionals, graduate and postdoctoral students

Venues: Unique locations for outdoor recreation and informal networking opportunities

Funding: ASBMB provides initial funding as well as complete meeting management!

Learn More About the Special Symposia Series and Proposal Submission Guidelines at

www.asbmb.org/specialsymposia

PROPOSALS DUE NOV. 1, 2011