Vol. 19 / No. 11 / December 2020
A SEARCH &A SPRINT Proteinases and their inhibitors
Feb. 24–26, 2021
This meeting covers diverse and vibrant fields of protease research, such as mechanistic studies on proteases in their molecular, cellular and organismic context. Sessions include: • proteolysis in cancer • proteolysis in neurosignaling and neurodegeneration • proteolysis in blood coagulation • discovery of protease substrates • mechanisms and engineering of proteases, ligases, their substrates and inhibitors
Abstract submission deadline: Jan. 11, 2021
Submit your abstract and register at: asbmb.org/meetings-events/proteinases-and-their-inhibitors CONTENTS
NEWS FEATURES PERSPECTIVES
2 26 47 PRESIDENT’S MESSAGE THE CELLULAR CONUNDRUMS THE DEATH PROJECT Barbara Gordon, ASBMB executive OF HEPATITIS C An excerpt from Nobelist Bob Lefkowitz’s director, to retire in 2021 Unraveling the genomic secrets of positive- new memoir strand RNA viruses 3 52 NEWS FROM THE HILL 32 ESSAY What the election results mean for science FROM BACTERIAL IMMUNITY Curbing the malpractice of curved grades TO SCIENTIFIC REVOLUTION and high-stakes exams 4 CRISPR’s sprint to the gold MEMBER UPDATE 54 42 MINORITY AFFAIRS HOLIDAY GIFT GUIDE A history-making administration — 8 ‘that believes in science’ IN MEMORIAM 44 ALEXANDRA NEWTON 56 9 FIVE QUESTIONS RESEARCH SPOTLIGHT A global champion of ‘the big puzzle’ — biochemistry A life devoted to teaching and research Wayne Fairbrother: “ You’ve got...to get outside of your comfort zone” 12 NEWS 26 12 Targeting two-faced nuclear receptors to fight cancer 15 JOURNAL NEWS 15 Bubbling biochemistry 16 Sphingolipids show potential as biomarkers for multiple sclerosis 47 18 Georgia Tech team publishes how-to for COVID-19 test kits 20 From the journals 32 HOLIDAY GIFTGUIDE 1 2
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3 5 DECEMBER 2020 ASBMB TODAY 1
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42 ASBMB TODAY DECEMBER 2020 DECEMBER 2020 ASBMB TODAY 43 PRESIDENT’S MESSAGE
Vol. 19 / No. 11 / December 2020
THE MEMBER MAGAZINE OF THE AMERICAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY Barbara Gordon, THE MEMBEROFFICERS MAGAZINE OFCOUNCIL THE AMERICAN MEMBERS SOCIETY FOR BIOCHEMISTRY ANDSuzanne MOLECULAR Barbour BIOLOGY Toni M. Antalis President Joan Broderick Charles Craik ASBMB executive director, GeraldOFFICERS Hart COUNCIL MEMBERS Matt Gentry PastGerald President Hart Squire J. Booker Susanna Greer President Victoria J. DeRose Wei Yang AudreyBlake Lamb Hill to retire in 2021 Secretary Jennifer DuBois JamesAudrey M. Ntambi Lamb Secretary Joan Conaway TakitaJames Felder M. Ntambi Sumter Celia A. Shiffer Toni TreasurerM. Antalis Kelly Ten–Hagen By Toni Antalis Treasurer Takita Felder Sumter EX-OFFICIO MEMBERS Kelly Ten-Hagen JoAnn Trejo t is with mixed feelings that I am EX-OFFICIO MEMBERS ASBMB TODAY EDITORIAL Robert S. Haltiwanger writing to let you know that the RobertCarla S. Haltiwanger Koehler ADVISORYASBMB TODAYBOARD EDITORIAL Co-chairs, 2020/2021 Annual Rajini Rao American Society for Biochem- Carla Koehler ADVISORY BOARD I MeetingCo-chairs, Program Committee2020 Annual Chair Rajini Rao istry and Molecular Biology’s long- Meeting Program Committee Cheryl Bailey AnaChair Maria Barral Chair, Education and Professional time executive director, Barbara A. Cheryl Bailey NatashaFloyd Brooks“Ski” Chilton Development Committee Chair, Education and KellyHenrik Chacón Dohlman Gordon, announced Nov. 16 that ProfessionalDaniel Development Raben BerondaPeter J.Montgomery Kennelly she will be retiring in early 2021. Chair, Meetings CommitteeCommittee BillBeronda Sullivan Montgomery Barbara has spent just about SoniaDaniel Flores Raben MelissaA. Maureen Vaught Rouhi Chair,Chair, Meetings Minority Committee Affairs Melissa Vaught her entire career at the society, and Binks Wattenberg CommitteeSonia Flores Binks W. Wattenberg we couldn’t have asked for a more Chair,Nicole Minority Woitowich Affairs ASBMB TODAY Chair, Science OutreachCommittee and ASBMB TODAY committed and caring leader. She Communication Committee AngelaAngela Hopp Hopp began working for the Journal of Susannna Greer Executive Editor Terri Goss Kinzy Executive Editor Chair, Public Outreach [email protected] Biological Chemistry in 1972 and Chair, PublicCommittee Affairs [email protected] Advisory Committee ComfortComfort Dorn Dorn went on to manage the society’s Matthew S. Gentry ManagingManaging Editor Editor Chair,Ed EisensteinPublic Affairs meetings and its journals before be- [email protected]@asbmb.org Barbara A. Gordon has been executive director of Chair, MembershipAdvisory Committee Committee ing appointed executive director in LaurelJohn Oldach Arnst the ASBMB since 2003. SusanSandra Baserga Weller ScienceScience Writter Writer 2003. During her tenure, she over- Chair, WomenChair, in Biochemistry Publications [email protected] and Molecular Biology [email protected] saw the journals’ transition to on- Committee Laurel Oldach Committee Ed Marklin I thank her for her exceptional service Lila M. Gierasch Science Writter line publishing and, most recently, Web Editor Editor-in-chief,Sandra Weller JBC [email protected] to the society and congratulate her on [email protected] their transition to open access. She Chair, Publications Ed Marklin A. L. Burlingame her well-deserved retirement. Committee Web Editor also oversaw the formation of new Editor, MCP Allison Frick Lila M. Gierasch Multimedia [email protected] and Social Media committees and programs, such as The Council will soon begin the NicholasEditor-in-chief, O. Davidson JBC ContentAllison Manager Frick search process for a new executive Editor-in-chief, JLR [email protected] Specialist the undergraduate degree-accred- A. L. Burlingame [email protected] director and will keep you updated on Kerry-AnneEditor, MCP Rye Barbara Gordon itation program and certification Editor-in-chief, JLR Barbara Gordon Nicholas O. Davidson Executive Director its progress. We will work closely with [email protected] Director exam, the IMAGE grant-writing Editor-in-chief, JLR [email protected] workshop, and the new MOSAIC Barbara, the headquarters staff and Kerry-Anne Rye the committees to ensure that there is Editor-in-chief, JLR program for diverse young investi- gators. Her list of accomplishments a smooth transition. is long and impressive. ForFor information information on on advertising, advertising, contact contact Pharmaceutical Pharmaceutical Barbara has been tremendously Toni Antalis Toni Antalis Media Inc. at 212-904-0374 or [email protected]@pminy.com.. supportive and encouraging to all ([email protected]) is a professor of physiology members of our ASBMB com- at the University of Maryland munity, and we will most certainly School of Medicine, where she miss her. She has freely shared her is also the associate director for training and education www.asbmb.org/asbmbtodaywww.asbmb.org/asbmbtoday wisdom, intelligence and humor for the Greenebaum Cancer PRINT ISSNISSN 2372-0409 2372-0409 with all who have had the pleasure Center and the director of the of working with her. On behalf of graduate program in molecular ArticlesArticles published published in ASBMB in ASBMB Today Today reflect reflect solely solely the authors’the authors’ views viewsand not medicine. She began her term and not the official positions of the American Society for Biochemistry and the official positions of the American Society for Biochemistry and Molecular the Council and all who have ben- as the ASBMB’s president on BiologyMolecular or Biologythe institutions or the institutions with which with the authorswhich the are authors affiliated. are affiliated. Mentions of productsMentions or of services products are or not services endorsements. are not endorsements. efited from working with Barbara, July 1.
2 ASBMB TODAY DECEMBER 2020 NEWS FROM THE HILL What the election results mean for science By Benjamin Corb
he election of Joseph R. Biden In the Obama administration, the Federal science agencies Jr. as the 46th president marks OSTP director was elevated to Cabi- Tthe end of a bitter campaign net-level importance; the Trump Agencies such as the National season and leaves in its wake a divided administration has devalued the Institutes of Health and National electorate struggling to survive a position. Science Foundation have seen their pandemic that has killed hundreds More immediately, a President budgets increase over the past four of thousands of Americans and has Biden could reverse executive orders years, a period that included a stalled the economy in ways not seen issued by Trump that have harmed split Congress and a White House in more than a generation. the American scientific enterprise. hostile to investments in science. Biden can act on restrictions on For example, the NIH’s budget Biden sets the tone immigration, proposed changes to has increased 45% since fiscal year visa timing rules and restrictions on 2016 — a trend that is unlikely to The contrast between President- federal support for research utilizing change anytime soon. elect Biden and President Donald embryonic stem cells, none of which Finally, the NSF director serves Trump has been stark. While Trump require congressional approval. a six-year term in order to keep the spent recent months downplay- position nonpolitical. The current ing the pandemic, Biden named a Congress still up in the air director, Sethuraman Panchana- COVID-19 task force on his first than, was appointed by Trump in “work day” of the transition, bring- While the presidential election’s late spring. I don’t expect him to be ing together 12 experts on disease outcome is certain, the balance of replaced, but I do anticipate that the and public health to begin develop- power in the U.S. Congress remains Biden administration will seek to ing a pandemic response plan to be in limbo. appoint a new head to the NIH. implemented on Day One of his Democrats maintain their major- Francis S. Collins, appointed by presidency. Biden also encouraged all ity in the U.S. House of Representa- President Barack Obama in 2009, is Americans to wear masks, a simple tives. The Senate, however, remains the second-longest-serving director gesture that public health experts have uncertain. Georgia had two open in the agency’s history. The incom- begged Trump to make. Senate seats this election, and in ing administration might consider Biden has promised “disciplined, both cases neither candidate received looking for more diversity in the trustworthy leadership grounded in 50% of the vote, triggering a pair of leadership. The NIH has had only science,” which I interpret to mean runoff elections. one woman director (Bernadine more subject matter experts at the The anticipated Senate makeup Healy from 1991 to 1993) since its helms of agencies such as the Envi- favors Republicans 50–48, with the founding in the 1880s. ronmental Protection Agency and two Georgia seats unsettled. Repub- science programs throughout the licans need to win only one of those Benjamin Corb (bcorb@asbmb. federal government. I expect the next Georgia seats to retain their major- org) is the ASBMB’s director of public affairs. Follow him on director to the White House Office of ity, while Democrats need both to Twitter @bwcorb. Science and Technology Policy, who earn a 50–50 tie; Vice President- acts as the science adviser to the presi- elect Kamala Harris will be able to dent, will play a more prominent role. cast tie-breaking votes.
DECEMBER 2020 ASBMB TODAY 3 MEMBER UPDATE
Canadian society honors to scientific societies including the In this half-time position, which Cole, Fairn American Association for Cancer began in September, Montgomery Research and the American Society will work on grants, cross-college Susan Cole, a professor in the de- for Pharmacology and Experimental and multi-institutional research partment of pathology and molecu- Therapeutics. She has been an edito- projects and the current phase of the lar medicine at Queen’s University in rial board member for the Journal Global Impact Initiative to recruit Kingston, Ontario, and Greg Fairn, of Biological Chemistry and several new research faculty to MSU. Doug an associate professor of surgery and other journals, received multiple Gage, interim vice president for the biochemistry at the University of awards and is a fellow of the Royal office, said, “Beronda’s expertise as a Toronto, are among the 2020 recipi- Society of Canada researcher and administrator, as well ents of awards from the Canadian and the Canadian as her deep connections with federal Society for Molecular Biosciences. Academy of Health funding agencies, will be a tremen- Cole received the society’s Jeanne Sciences. dous asset to help us pursue these Manery-Fisher Memorial Award Fairn, who important activities.” for excellence in science, and Fairn joined the faculty A professor in the MSU-U.S. won the New Investigator Award for at the University of Department of Energy plant research outstanding accomplishments by a Toronto in 2012, lab, Montgomery has appointments researcher who has been a PI for less FAIRN studies cellular in the departments than 10 years. membranes in a of biochemistry and Cole, who holds the Bracken chair variety of physiological states. One molecular biology, in genetics and molecular medi- line of research concerns contact sites and microbiology cine, studied pharmacology and did between the endoplasmic reticulum and molecular ge- postdoctoral training at the National and other membranes, including the netics. Her primary Institutes of Health before joining cellular membrane and the phagolyso- lab-based research the Queen’s faculty some, and how these contacts are is focused on the in 1994. She stud- regulated by the lipids found in each MONTGOMERY responses of photo- ies the biochem- membrane. Fairn also pursues an in- synthetic organ- istry of chemo- terest in the interaction between host isms such as plants and cyanobacteria therapy resistance cells and pathogens, including the to external light cues. Her interests in cancer; her lab study of how macrophage sense and include biosynthesis and biochemical discovered a mem- eliminate bacterial and fungal patho- function of biliproteins in photosyn- brane protein in gens and the importance of protein thetic organisms, intercellular phyto- COLE the ATP-binding lipidation in the process. chrome signaling and light-dependent cassette family, In 2017, Fairn won the American regulation of morphology. called multidrug resistance protein Society for Biochemistry and Mo- Montgomery’s research extends 1, or MRP1, that can render cancer lecular Biology Walter Shaw Young beyond biology, following a theme cells resistant to many drugs when Investigator Award. of understanding how individuals expressed. Subsequently, they found perceive, respond to and are impacted that beyond drug efflux, MRP1 also Montgomery joins by their environments. She studies exports the antioxidant glutathione mentorship and faculty development and numerous immune signaling MSU research to develop evidence-based strategies molecules including leukotrienes and and innovation office to foster equity and inclusion in aca- prostaglandins. The lab also studies demia. She served as assistant provost other homologous proteins in the Beronda Montgomery, a profes- for faculty development at MSU from MRP family. sor and plant biology researcher at 2016 to 2020. The award also recognizes Cole’s Michigan State University has been Montgomery was elected to the track record of mentorship (she named interim assistant vice president American Academy of Microbiology has trained more than 60 graduate of the MSU office of research and students and postdocs) and service innovation. CONTINUED ON PAGE 6
4 ASBMB TODAY DECEMBER 2020 MEMBER UPDATE
ASPET names new fellows
The American Society for Pharmacology and Experi- Gudas holds leadership positions within ASPET, the mental Therapeutics, or ASPET, recently inducted a new American Association for Cancer Research and several class of fellows. Six American Society for Biochemistry other cancer research organizations. and Molecular Biology members were included in the list Eric Johnson, a professor in the department of mo- of 19 fellows, honored for their excellence in pharmacol- lecular medicine at the Scripps Research Institute, studies ogy research and in service to the field. cytochrome P450 enzymes, which are key enzymes in ste- Joan Heller Brown, chair of the pharmacology depart- roid biosynthesis and drug metabolism. P450 enzymes are ment at the University of California, San Diego, studies also involved in processing other xenobiotics, regulating the signaling action of G protein–coupled receptors, or blood pressure, and inflammation. His lab determined GPCRs, which transduce extracellular signals into activa- the first crystal structure of a membrane P450 enzyme tion of intracellular enzymes. Her work focuses on cyto- and has continued to characterize the structures of mam- skeletal, growth and gene-expression changes downstream malian P450s in complex with various substrates and of GPCRs in vascular and heart cells. Brown also serves as inhibitors. Johnson serves on editorial boards of several principal investigator of the UCSD graduate training grant journals in biochemistry and pharmacology. in pharmacology, one of the nation’s largest, and directed John Scott, chair of the pharmacology department at the university’s graduate program in biomedical sciences the University of Washington, discovered scaffold pro- for years. teins known as A-kinase anchoring proteins, or AKAPs, Marc Caron, a professor at Duke University, studies that bind to and organize protein kinase A and related G-protein coupled receptors, with particular interest in signaling molecules. The signaling complexes that AKAPs neurotransmitter receptors. Caron developed many early generate have been found to regulate synaptic transmis- techniques for GPCR purification and visualization, then sion, insulin secretion and cardiac cell contraction. Scott, moved into studying accessory proteins that modulate a fellow of the Royal Society London, won the ASBMB’s receptor function. Now his lab is interested in selective 2008 William C. Rose Award for his excellence in men- signaling, using allosteric modulators to activate certain toring and has organized many conferences over the years. signaling outcomes while blocking others. Such approaches David Sibley could be used, for example, to design non-addictive , a section chief and senior investigator pain relievers. at the National Institute of Neurological Disorders and Stroke, studies the pharmacology of G protein–coupled Lorraine Gudas, chair of the pharmacology depart- receptors, especially those that respond to dopamine. ment at Weill Cornell Medicine, studies retinoid com- He also works on biased signaling and allosteric ligand pounds such as vitamin A, along with the receptors and development, leading to agonists and antagonists specific downstream effectors through which they signal. Because for certain dopamine receptor types. He has served as the retinoids can cause differentiation, she has also pursued president of ASPET and as an editor of eight scientific research into carcinogenesis and potential therapeutic uses journals in pharmacology and biochemistry, and has for stem cells. In addition to chairing her department, edited several books.
BROWN CARON GUDAS JOHNSON SCOTT SIBLEY
DECEMBER 2020 ASBMB TODAY 5 MEMBER UPDATE
CONTINUED FROM PAGE 4 replace structures built in the 1960s. of the drug Somavert, which is used in 2018 and recently was named one John Kopchick earned his bach- to treat acromegaly, a rare hormonal of Cell Press CrossTalk’s 100 Inspiring elor’s and master’s disorder. His research focuses on the Black Scientists. She is a member of degrees at IUP and molecular biology of growth hormone the ASBMB Today editorial advisory his Ph.D. at the in relation to growth, obesity, insulin board and her most recent essay for University of Texas resistance, diabetes and aging. His the magazine was “To support or Graduate School lab also generated and characterized deny: mentoring or gatekeeping?” of Biomedical Sci- the world’s longest-lived laboratory ences in Houston. mouse. IUP breaks ground He then did post- Construction of Kopchick Hall KOPCHICK doctoral research at is scheduled for completion in fall for Kopchick building the Roche Institute 2023. The four-story building will A groundbreaking ceremony was of Molecular Biology and worked as be equipped with an anatomy lab, held in September for John J. and a researcher at the Merck Institute of greenhouse, imaging lab, laser lab, Char Kopchick Hall, a science re- Therapeutic Research. In 1987, he planetarium and vivarium. The search building at Indiana University accepted an endowed professorship at university expected to reach the goal of Pennsylvania. The Kopchicks, both Ohio University where Char Kop- of raising $75 million for the building IUP alumni, pledged $23 million in chick is the assistant dean of students. in October. Any funds left over after 2018 for the new building, which will John Kopchick is the co-inventor construction will be used for scholar- ships and undergraduate research. “Without my education here, I Tufts names research center for Levy wouldn’t be in a position to give any- one money,” John Kopchick said dur- Tufts University has renamed its Center for Integrated Management of ing the dedication ceremony at IUP. Antimicrobial Resistance after the late Stuart B. Levy, a researcher who “It is a way of giving back, looking launched the movement for antibiotic stewardship. forward and paying ahead. We are Levy, a molecular and microbiologist who taught and practiced medi- very proud and fortunate to be able to cine at Tufts for 47 years, began his research into antibiotics in the 1970s. do this.” With colleagues, he reported that antibiotics in animal feed could select for resistant bacteria, which could then be transferred to humans. Over IFCC honors Sacks for lab the years he studied the molecular mechanisms of tetracycline efflux, the genetics of multidrug resistance and other related topics. medicine, patient care His research led Levy to conclude that rampant overuse of antibiotics, David Sacks, a senior investigator especially in agriculture, threatened both the drugs’ efficacy and pub- at the National Institutes of Health, lic health. He became an activist for has received the 2020 International antibiotic stewardship, meeting with Federation of Clinical Chemistry and regulators, founding a nonprofit and in Laboratory Medicine Distinguished 1992 publishing a book, “The Antibiotic Award for Laboratory Medicine and Paradox: How miracle drugs are destroy- Patient Care. ing the miracle.” The award recognizes Sacks’ work Remembering Levy, his colleague with patients who have diabetes, John Leong, who is on the center’s lead- notably his contribution to standard- ership team and led the push to rename, LEVY izing measurement of glycated hemo- said, “He combined fundamental globin. Because sugars at sufficient research and clinical practice and then could look down the road and concentration can bind spontane- see the consequences of unregulated, unthoughtful use of antimicrobial ously with hemoglobin to produce a agents. He changed the way we think about how we use antibiotics.” product with a month-long half-life, Levy died in September 2019 at the age of 80, about a year after retir- hemoglobin glycation is a good read- ing from Tufts. out for patients’ blood sugar levels over time.
6 ASBMB TODAY DECEMBER 2020 MEMBER UPDATE
Sacks attended medical school at the University of Cape Town in Virtual seminar honors 100-year-old Eddy Fischer South Africa and completed residen- cies in internal medicine and clini- Nobel laureate Eddy (Edmond) Fischer, an emeritus professor at the cal pathology in the U.S. He taught University of Washington and a member of the American Society for and ran a lab at Harvard University Biochemistry and Molecular Biology since 1955, recently celebrated his and Brigham and Women’s Hos- 100th birthday. pital before coming to the NIH as The university couldn’t throw the party it had planned for Fischer in a senior investigator and chief of April, but Trisha Davis, chair of the UW department of biochemistry, or- clinical chemistry ganized a two-day virtual seminar on Oct. 29 and 30, featuring 12 speak- in 2011. He is a ers from throughout Fischer’s scientific life. Among them was his grand- past president of daughter Elyse Fischer, a graduate student at Cambridge University, who the Academy of spoke about her research on how phosphorylation affects the structure of a Clinical Labora- protein involved in the mitotic spindle checkpoint. A number of ASBMB tory Physicians members also spoke, including Tony Hunter, Rachel Klevit, Alexandra and Scientists, an Newton, Nicholas Tonks, Susan Taylor and John Scott. associate editor at Eddy Fischer was born in Shanghai to European expatriates in 1920, SACKS the journal Clinical then attended school and university in Switzerland. He came to the U.S. Chemistry and a in 1950 to work at the California Institute former editorial board member for of Technology. When he was offered a the Journal of Biological Chemistry. position at the University of Washington, In the laboratory, his research focuses Fischer and his wife found that Seattle re- on signal transduction, with particular minded them of Switzerland, so he moved interest in calcium signaling. to UW and remained there for the rest of The IFCC is a federation of profes- his career. sional societies in the field. This award Fischer shared the 1992 Nobel Prize recognizes a scientist who has made a in Physiology or Medicine with colleague FISCHER significant contribution to laboratory Edwin Krebs for their joint description of medicine that improves worldwide the importance of protein phosphorylation in regulating protein activity, clinical medicine and patient care. signaling and cellular processes. Linda Buck, a fellow Nobel laureate from the Fred Hutchinson Cancer Radford honored with OBE Research Center, who has known Fischer for decades, said during the seminar, “In addition to being brilliant, Eddy is one of the most exuberant For her services to molecular people I’ve ever met.” biology research, Sheena Radford, Astbury professor of biophysics at the University of Leeds, has been named on the mechanics of protein folding Medical Sciences, the Royal Society a civil officer of the and how misfolding leads to cellular and the European Molecular Biology Order of the British dysfunction and disease. Current ar- Organization. Honors include the Empire, among eas of study include protein misfold- Biochemical Society Colworth Medal, the 2020 Queen’s ing and assembly into amyloid, and the Royal Society of Chemistry Astra Birthday Honours the role of chaperones and the BAM Zeneca Prize and Cornforth Award, announced in complex in folding mechanisms. and the Protein Society Branden October. Radford earned her bachelor’s Award. As director of the degree and Ph.D. at Cambridge The Queen’s Birthday Honours for RADFORD Astbury Centre for University. She was a reader at Leeds the U.K. are traditionally announced Structural Biology from 1998 to 2000 before being as part of Queen Elizabeth II’s official at Leeds, Radford leads a group of named a professor, and she has led birthday celebration in June but were researchers who investigate the mo- the Astbury Centre since 2012. delayed this year because of the CO- lecular basis of life. Her work focuses She is a fellow of the Academy of VID-19 pandemic.
DECEMBER 2020 ASBMB TODAY 7 IN MEMORIAM
Elie Shneour Gregory R. Schonbaum
The American Society for The American Society for Biochemistry and Molecular Biochemistry and Molecular Biology recently learned that Biology recently learned that emeritus member Elie Alexis Gregory Richard Schon- Shneour, a neurochemist and baum, an emeritus member biophysicist who joined the who joined the society in society 50 years ago, died 1973, died June 26, 2019 at March 14, 2015 in San Diego. age 91 in Memphis, Tennessee. A biochemist for more Born in France on Dec. 11, 1925, Shneour was than 40 years, his work focused on understanding raised in a Paris suburb. His father was a noted Yiddish enzymatic mechanisms. poet and writer, Zalman Shneur. When Nazi Germany Born February 21, 1928 in Lvov, Poland, Schon- occupied France in 1940, the family escaped to Spain baum spent the years of World War II in hiding after and then landed at Ellis Island in 1941. his parents were arrested and sent to concentration After graduating from high school in New York, camps. After the war, he immigrated to London where Shneour joined the Army and attained the rank of he earned his Ph.D. in organic chemistry at the Uni- captain. He earned a bachelor’s degree in biology versity of London and met his future wife, Madeleine from Bard College, a master’s in biochemistry from Frydman. the University of California, Berkeley and a Ph.D. in The couple crossed the Atlantic, and Schonbaum biochemistry at UCLA. held postdoctoral fellowships at the Johnson Founda- Shneour began his career as a researcher and tion at the University of Pennsylvania in Philadelphia, lecturer at Stanford University, then as an assistant with Britton Chance, and at the Illinois Institute of professor at the University of Utah. He continued his Technology with Myron Bender. He held positions in research at the City of Hope National Medical Center Pennsylvania and at the University of Alberta in Ed- in Los Angeles and then moved to La Jolla in 1971 to monton, Canada. During a sabbatical at the University serve as director of research for Calbiochem. In 1975, of California, Berkeley, he worked with Lester Packer, a he formed Biosystems Associates (later Biosystems world leader in the study of antioxidants. Research Institutes), a scientific consulting company, As a researcher at St. Jude Children’s Research which he ran until his retirement in 2014. Hospital, Schonbaum spent almost 20 years continuing A prolific writer and a fellow of the Committee his studies on the enzymatic mechanisms of hemo- for Skeptical Inquiry, Shneour authored many articles proteins and seeking treatments for the side effects of on science and politics. His published books included chemotherapy. In the 1980s, he patented a method for “Life Beyond the Earth” and “The Malnourished Mind,” alleviating kidney damage from the chemotherapy drug and he completed a manuscript on 20th-century his- cisplatin with a polar dithiocarbamate compound. tory, tentatively titled “Margins of Error.” In a final contribution to science, Schonbaum do- Shneour was a gourmet cook and a serious nated his body to the Medical Education and Research photographer. He once owned a Hasselblad camera Institute. He is survived by his wife of 65 years, Mad- used on the moon by NASA. He was survived by his two eleine Schonbaum; his children Pierre, Chris (Eunju) children, Mark and Alan; and his three grandchildren, and Danielle; and his grandchildren, Alex and Rachel. Collin, Luke and Trey. He was predeceased by his son Michael.
8 ASBMB TODAY DECEMBER 2020 RESEARCH SPOTLIGHT A life devoted to teaching and research Karlett Parra’s scientific journey has taken her from Venezuela to New Mexico By Gelareh (Abulwerdi) Vinueza COURTESY OF KARLETT PARRA arlett Parra remembers when she first became interested in K academia. “In high school, I graded multiple-choice exams with my aunt,” she said. Her aunt, Omaira Figueroa, an embryology and histology professor at the Universidad de Carabobo in Venezuela, gave Parra more than tests to grade: “My aunt mentored me for my first research project in high school that made me fall in love with research.” The project involved feeding a vegetable diet to two rabbits (the control group) and a high-fat diet to another two rabbits. The experiment Karlett Parra speaking at the Executive Leadership in Academic Medicine Program in 2017. ended quickly when the rabbits on the high-fat diet died, but this project her teenage years. “My parents often As an undergraduate, I was Parra’s first step in her scientific reminded me of the value of educa- ‘‘ career. “I learned to test a hypothesis, tion and the importance of pursuing a had my first biochemistry quantify and analyze histology data, college degree,” she said. research experience, and it and make conclusions,” she said. While pursuing her bachelor’s Figueroa died in 2009. In addition degree at Simón Bolívar University, was love at the first sight.’’ to starting her niece in research, her she became involved in research. legacy includes changing the univer- “As an undergraduate, I had my first from the parasitic nematode Ascaris sity’s curriculum to add research to biochemistry research experience, suum. She remembers working so the didactic bioanalysis program and and it was love at the first sight,” she late at night to isolate proteins and securing funds to build a bioanalysis said, adding that the chromatography measure the activity of enzymes that education building. The under- and Western blotting used to purify her mother had to pick her up after graduate research program that she and visualize proteins were of great everyone else had left the building. “I established was named Jornadas de interest. “The fact that I could ‘see’ a loved every moment of working in the Investigacion en Pregrado Licenciada protein fascinated me.” research lab,” she said. Omaira Figueroa in her honor. In addition to her committed Parra went on to earn her master’s Born and raised in Caracas, coursework, Parra joined a laboratory in biochemistry from Simón Bolívar Venezuela, Parra said the rest of her so she could conduct research and University and decided to pursue a family also noticed her enthusiasm learn new methods such as purifying Ph.D. so she could continue doing for science and cultivated it from mitochondrial F1–ATPase complex research. One of her undergraduate
DECEMBER 2020 ASBMB TODAY 9 RESEARCH SPOTLIGHT COURTESY OF KARLETT PARRA professors, Jose Bubis, connected her with scientists he knew in Syracuse, New York. In 1992, Parra moved to the U.S. to start her Ph.D. training in biochemistry and molecular biology at the State University of New York Upstate Medical University in Syra- cuse under the supervision of Patricia Kane, who became her mentor. Parra’s dissertation research focused on studying the regulation of a conserved ATP-driven proton pump called vacuolar H+-ATPase, or V-ATPase, in yeast. V-ATPase can Karlett Parra is chair of the biochemistry and molecular biology department at the University of New pump protons across the membranes Mexico. of mammalian cells; hence, it can acidify the intracellular compartment the department of biochemistry and community. of cell organelles such as lysosomes molecular biology. “Classrooms (at UNM) are and endosomes. By this time, Parra was an associ- composed of mainly underrepre- After a short postdoc at SUNY ate professor, and the new posi- sented communities, with about 55% Upstate, Parra taught biology in tion was for an assistant professor, Hispanic population, 6% Native LeMoyne College and moved to Ball but she saw it as a challenge and a Americans, and the rest a mix of other State University in Indiana to take a way to grow in her career. In New races,” Parra said. “Seeing these stu- full-time position as a tenure-track Mexico, she would be part of a dents advance in their lab work and assistant professor in the chemistry medical school where her research coursework is very exciting for me, department. She enjoyed teaching would have a broader biomedical and I enjoy inspiring them to pursue undergraduates and graduates, but impact than at BSU, a primarily un- careers in the life sciences.” six years later, a career opportunity dergraduate institution. Moreover, Parra has continued her studies of presented itself at the University of she was excited to work with a more V-ATPase, which plays an important New Mexico School of Medicine in diverse student body and research role in many pH-dependent cellular
COURTESY OF KARLETT PARRA processes. Its function is linked to the understanding and treatment of many disorders, including viral infections, neurodegenerative diseases, diabetes and cancer. For example, in prostate cancer, Parra’s lab found that inhibi- tion of V-ATPase affects the hypoxia- inducible factor-1-alpha function and androgen receptor expression, making V-ATPase potentially beneficial in treatment. Continuing her interest in bioener- getics, Parra studies the communica- tion mechanisms between glycolytic activity and V-ATPase function. “This communication is crucial,” she said, “because it allows cells to adjust V- Karlett Parra (left) with her aunt, Omaira Figueroa, photographed in 1993 when Parra was a new gradu- ATPase assembly, activity and mem- ate student in Syracuse, New York. brane distribution during periods of
10 ASBMB TODAY DECEMBER 2020 RESEARCH SPOTLIGHT COURTESY OF KARLETT PARRA low and high energy demand.” After five years at UNM, Parra was named chair of the biochemistry and molecular biology department — a new challenge that required her to acquire a whole new set of skills. “I am not only managing my lab and my students, but I am respon- sible for the success of the whole department,” she said. “I enjoy working with the junior faculty and seeing their progress to have a posi- tive impact on science education.” Parra admires the late Venezuelan physician–scientist Jacinto Con- vit, who developed a vaccine for leprosy. In 1988, he was reportedly in the running for the Nobel Prize in physiology or medicine for this work. Parra wishes she could have met Convit and asked about his research. “What were some of the limitations that he overcame?” she wondered. “How did he establish such a successful research program that impacted so many lives consid- ering the very few resources he had Taking an outdoor break during a FASEB Science Research Conference meeting are, left to right, Summer at that time?” Raines Hayek (then a postdoc, now a lecturer at UNM), Karlett Parra and Ph.D. students Chun-Yuan Chan Since 2007, Parra’s family, includ- and Yamhilette Licon Munoz. ing her mother, Judith, and her brother, Carlos, have reunited with I have cooking questions, I contact art district. She hopes that one day her in Albuquerque. Outside of my cousin who is a chef in Florida, she will have visited all 300 galleries work, Parra enjoys hiking, working or I refer to her cookbook.” in the city. out and cooking with her family. Parra also enjoys visiting contem- “I love spending my weekends at Her favorite dish to prepare is Span- porary and traditional Southwestern the galleries,” she said, “because it ish paella, and she has a special ad- art galleries, especially those on makes me get a fresh perspective when vantage in the kitchen: “Whenever Canyon Road in Santa Fe’s historic I return to work.”
Gelareh (Abulwerdi) Vinueza ([email protected]) About the Research Spotlight graduated with her Ph.D. from the molecular medicine program The American Society for Biochemistry and Molecular Biology’s Research at the University of Maryland, Baltimore. She is currently a Spotlight highlights distinguished biomolecular and biomedical scientists from policy fellow at the Food and Drug Administration. She has diverse backgrounds as a way to inspire up-and-coming scientists to pursue been an ASBMB volunteer writer careers in the molecular life sciences. Eligible candidates include Ph.D. stu- since 2018 and is passionate about science communication dents, postdoctoral fellows, and new or established faculty and researchers. To and science policy. Outside of work, she enjoys photography, nominate a colleague for this feature, contact us at [email protected]. hiking and cooking. Follow her on Twitter @gelareh_science.
DECEMBER 2020 ASBMB TODAY 11 NEWS Targeting two-faced nuclear receptors to fight cancer
By Lisa Nicole Learman TEXAS A&M COLLEGE OF VETERINARY MEDICINE & BIOMEDICAL SCIENCES
or small-molecule cancer drugs, context is every- thing. No one is more aware of this than Stephen FSafe, who designs such drugs in his molecular and cellular oncology lab at Texas A&M University. Many of the drugs his team synthesizes target nuclear recep- tors, which can exhibit either pro- or anti-cancer activity depending on the tissue type. A native of Canada, Safe initially studied geology at Queens University. After a harrowing experience with a summer job in a uranium mine, he decided to switch fields. “It was easy to get killed by someone blowing you up with dynamite or rocks falling on you,” he said, “so I thought it was time to change, and I went into chemistry.” Stephen Safe, pictured in his lab, is the Syd Kyle chair of veterinary Safe’s work as a chemist led him to a biological target medicine and a professor of veterinary physiology and pharmacology, that is now the focus of his lab, the aryl hydrocarbon re- biochemistry and biophysics, and molecular and cellular medicine at ceptor. He and his colleagues initially became interested Texas A&M University. in how organochlorine compounds such as dichloro- diphenyltrichloroethane, better known as DDT, and a drug that binds the estrogen receptor. In breast tumors, polychlorinated biphenyls, or PCBs, affect the environ- tamoxifen blocks estrogen receptors and significantly ment. They synthesized derivatives of the compounds to reduces cancer development. After using the drug for identify how different parts of the molecular structure decades, researchers found that it caused a small but contribute to organochlorine toxicity. For one such meaningful increase in the risk for endometrial cancer. chemical, dioxin, Safe said, “It turned out that the toxic- This is because in the uterus, tamoxifen stimulates estro- ity was related to binding affinity to this new receptor gen receptors, which promotes cancer. According to Safe, called the aryl hydrocarbon receptor.” the potential for antagonistic functions of small-molecule Physiologically, the aryl hydrocarbon receptor, or drugs in different tissues is something “you don’t know AhR, senses nutrient byproducts to regulate cell growth offhand and you can’t predict.” and response to inflammation. Safe and his team deter- Much like the estrogen receptor, designing selective mined that although ligands of the AhR can be toxic, receptor modulators for the AhR can feel like trying to some could wipe out tumors in a rat model of breast hit a moving target. Depending on the context, AhR cancer. They began to develop what Safe refers to as receptor activity can help or hurt cancerous cells. In head “selective receptor modulators,” compounds that bind and neck tumors, the receptor is pro-cancer, while in the receptor and inhibit tumor growth but are relatively gastrointestinal tumors, it’s anti-cancer. Safe sees the dual nontoxic. nature of the AhR as a challenge but also an opportunity. Designing these compounds is not straightforward. “The beauty of it is you can design selective AhR modu- Transcription factors often have different functions in lators as agonists or antagonists,” he said. “So, if the AhR different tissues, so developing safe and effective drugs is a good thing, you treat with an agonist, and if the AhR can be tricky. Safe’s favorite example of this is tamoxifen, is a bad thing, you treat with an antagonist.”
12 ASBMB TODAY DECEMBER 2020 NEWS
In a 2019 paper, Safe’s lab characterized the role of paper have been able to reconcile the apparent contradic- the aryl hydrocarbon receptor in glioblastoma as anti- tion in their results. cancer, disproving a previous Nature paper. The lab In addition to their AhR research, Safe’s lab designs didn’t set out to disprove the original finding. Safe’s team small-molecule cancer drugs that target other nuclear was helping Sharon Michelhaugh and Sandeep Mittal, receptors, oncogenic long noncoding RNAs and the glioblastoma researchers at the Karmanos Cancer Center PDL-1 immune checkpoint inhibitor. They also have in Detroit, who were interested in the natural AhR started to identify over-the-counter drugs with AhR ligand kynurenine but were having a hard time getting receptor binding activity. Safe’s group hopes that these their invasion assay to work. When Safe’s lab looked into drugs, which are already FDA-approved, could be used it for them, they could not replicate the published results as cancer therapeutics. demonstrating that kynurenine and its action on AhR “The one we’ve used the most for glioblastoma is were pro-invasion in glioblastoma. In fact, their compre- Prilosec, the proton pump inhibitor,” Safe said. In July, hensive study yielded the opposite conclusion. Knocking he and his collaborators published a study showing that out the AhR increased invasion, suggesting the receptor Prilosec inhibits glioblastoma cell invasion and tumor exhibits anti-cancer activity. growth by promoting aryl hydrocarbon receptor activity. Safe and his team of scientists repeated the experi- The lab has expanded its molecular targets, led always ment countless times. “We just didn’t believe it,” he by their work with AhR. “Every time you go to an AhR said. The Nature paper had characterized the AhR as conference, enormous new things come out,” Safe said. pro-cancer in glioblastoma. Safe said his lab “had some “It’s an amazing receptor.” trouble getting (our) paper published because we were disproving a Nature paper by a good group.” Lisa Nicole Learman ([email protected]) is a After characterizing the AhR knockout in many Ph.D. candidate studying molecular neuroscience at models at both functional and genomic levels, bolstered Johns Hopkins University School of Medicine. She is passionate about dystopian fiction, increasing public by their finding that one of their AhR agonists inhib- understanding of science and the music of Charles ited glioblastoma invasion, Safe was sure they were Mingus. Follow her on Twitter @LearmanLisa. right. Neither his lab nor the authors of the original
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DECEMBER 2020 ASBMB TODAY 13 Don’t forget to renew your ASBMB membership! Over the past 100 years, the ASBMB has grown and changed with the times to become the supportive community of discoverers that it is today.
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14 ASBMB TODAY DECEMBER 2020 JOURNAL NEWS Bubbling biochemistry Understanding the components of sparkling wine
By Laurel Oldach plex sugar molecules. As wines age, their proteins and glycopeptide constituents change. hether or not your holi- According to Ben Schulz, the profes- day celebrations involve sor who led the work, changes late in Wimbibing, the cultural link the aging process, when “no biol- between champagne flutes and fes- ogy should be happening,” probably tivities is strong. The fizz and pop of sparkling wine give breaking out the depend on the biophysics of protein bubbly a special pizzazz. solubility. Glycosylation can make a In the first glycoproteomics study peptide more water-soluble and less of its kind, a research team reports likely to clump into sediment. in the journal Molecular & Cel- Similar principles may guide a lular Proteomics that glycoproteins wine’s propensity to gush. Researchers are an important part of keeping previously had found that a yeast cell those bubbles in solution. Cassandra wall protein called seripauperin 5 can Pegg and colleagues at the Univer- stabilize foam; this and related pro- sity of Queensland put a variety of teins were among the most abundant sparkling wines under the micro- that Schulz’s team identified. scope — or, more accurately, into “It’s not completely understood,” the mass spectrometer — in hopes Schulz said of the protein’s foam- that the work would lead to better stabilizing effect. “But from a bio- wine-making methods. yeast and sugar and seal it all into physical standpoint, it makes sense: “Sparkling wine is really difficult a bottle to trap the carbon dioxide Glycans tend to be hydrophilic, and to pipette,” Pegg, a postdoctoral the yeast produces. The yeast strain, peptides hydrophobic.” By clustering researcher in Ben Schulz’s lab, said. grape blend and tweaks to the at the interfaces between liquid and “We have had some sets of samples production process can affect the gas, small glycopeptides could affect a that were gushing” — that’s a wine- quality of the final product — but wine’s surface tension and change the biz term for when bubbles won’t stay the process is often a matter of trial rate at which dissolved gas coalesces in solution — “and the tubes would and error. into bubbles and escapes. pop open in the lab.” To understand more about mo- By understanding the production Gushing, when champagne lecular attributes leading to positive methods that affect seripauperin 5 or cava comes foaming out of an prosecco properties, the researchers and other glycoproteins, Schulz said, opened bottle, entertained Pegg degassed samples of sparkling wine he hopes to work in the future with and her colleagues. But it’s less than that had been aged for different winemakers looking to optimize their desirable commercially: Winemakers periods or fermented with different products. want the dissolved gas to come out strains of yeast. They used proteomic DOI: 10.1074/mcp.RA120.002181 of solution slowly, making a bever- and glycoproteomic techniques to characterize the brews. Wine doesn’t age that continues to bubble until Laurel Oldach (loldach@asbmb. it’s finished. have much protein, and most of the org) is a science writer for the Sparkling wine’s carbonation proteins they found were secreted ASBMB. Follow her on Twitter @LaurelOld. results from two rounds of fermen- by yeast or found in yeast cell walls. tation. After producing a base wine, A surprisingly high proportion were winemakers mix in a solution of glycosylated, or modified with com-
DECEMBER 2020 ASBMB TODAY 15 JOURNAL NEWS Sphingolipids show potential as biomarkers for multiple sclerosis
By Deboleena M. Guharay ILENA GEORGE AND DANIEL REICH, NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE, NATIONAL INSTITUTES OF HEALTH
ultiple sclerosis is an immune- mediated disease affecting Mthe central nervous system. In MS, the myelin layer of the nerve cells is damaged by the immune system, creating plaques or lesions that cause problems in signal trans- mission between the brain and the rest of the body. According to the National Multiple Sclerosis Society, more than 1 million people in the U.S. live with MS. Symptoms include numbness of limbs, vision problems, fatigue and dizziness. There is no cure, but treatments might help to manage symptoms and disease progression. Scientists are looking for potential biomarkers to understand the stages of the disease’s development. Maria Podbielska, a researcher at the Ludwik Hirszfeld Institute of Im- munology and Experimental Therapy in Poland, has been working to iden- tify these biomarkers. Her interest in MS developed during her postdoctoral fellowship in Edward L. Hogan’s labo- ratory at the Institute of Molecular Medicine and Genetics in the Medical Axial MRI scans of the brain of a person with multiple sclerosis have been segmented into various College of Georgia, Augusta Univer- tissue types. sity, between 2005 and 2010. There, she worked on projects involving the pathological mechanisms of MS. biopsied MS population.” sheath and could be biomarkers to “MS is heterogeneous with respect Multiple sclerosis consists of two track these phases. to clinical, genetic and pathologic pathological processes: inflammation, In a recent paper in the Journal features,” Podbielska explained. or active phase, and neurodegenera- of Lipid Research, Podbielska and “Therefore, a set of verified and tion, or inactive or chronic phase. her colleagues wrote that they found specific biomarkers for each pattern Both phases begin from the onset of sphingolipid species as potential of immune-mediated brain damage the disease, but they develop at differ- biomarkers for the inflammatory needs to be developed in order to ent rates. Sphingolipids, or SLs, are an and neurodegenerative processes recognize them in the general non- important component of the myelin involved in MS pathology. They did
16 ASBMB TODAY DECEMBER 2020 JOURNAL NEWS
a sphingolipodomic analysis using Multiple sclerosis consists of “The most important observation high-performance liquid chromatog- is related to our discovery of some raphy–tandem mass spectroscopy in two pathological processes: kind of MS diagnostic ‘red flag’ — a postmortem specimens of normal- inflammation, or active phase, and striking increase of the ceramide- appearing white matter from healthy 1-phosphate levels in progressive MS central nervous systems and from neurodegeneration, or inactive or lesions,” she said. patients with active and inactive stages chronic phase. Both phases begin Podbielska plans to continue her of the disease. work to find more potential lipid Ceramide, or Cer, is an important from the onset of the disease, but biomarkers that might help to develop component of SL pathways. The re- therapeutic treatments for MS. searchers found various Cer metabolic they develop at different rates. DOI: 10.1194/jlr.RA120001022 forms in different proportions in the active and inactive MS lesions, which clearly showed different SL pathways the researchers noticed a different Deboleena M. Guharay involved in the active and inactive pathological scenario for inactive MS ([email protected]) earned her Ph.D. in chemistry phases of MS. nervous system damage, where the from Virginia Commonwealth The tissue studies implicated sphingomyelin-ceramide-hexosylce- University. She is very enthusias- sphingolipid biosynthesis in active ramide metabolic pathway could be tic and passionate about science communication. MS lesions, Podbielska said, but responsible for damage to neurons.
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JANUARY Cervical Health Awareness Month 1 ASBMB journals become open access 1 Deadline to submit an ASBMB Annual Meeting interest group proposal 4 Deadline to submit ASBMB fellows nominations 7 Abstract deadline for the ASBMB Annual Meeting held in conjunction JAN. with Experimental Biology 7 Deadline to apply for ASBMB Annual Meeting grants and awards 11 Abstract deadline for Proteinases and their inhibitors 24 International Day of Education
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DECEMBER 2020 ASBMB TODAY 17 JOURNAL NEWS Georgia Tech team publishes how-to for COVID-19 test kits
By Lisa Nicole Learman
n the spring of 2020, the U.S. ‘‘We wanted to do something for the cytosine, known as A, G, T and C. experienced severe shortages of whole world. The U.S. didn’t have The researchers made a chain of these ICOVID-19 tests, and a frustrated nucleotides that binds a part of the public wondered why testing kits were enough test kits, which made me viral genome through complementary so hard to produce. Georgia Tech base pairing, in which A’s bind to scientists took action, developing pro- think about other, poorer countries T’s and G’s bind to C’s. Finally, they tocols that can be used by laboratories with bad economies. added fluorescent tags to the end of to make COVID-19 test kits in many ’’ these DNA pieces so that when the settings and with many budgets. SARA FAHKRETAHA–AVAL viral genome is recognized and ampli- Loren Williams, a professor of fied by an enzyme, it can be detected chemistry and biochemistry, spear- by looking at the fluorescence signal. headed the effort, shifting his lab’s labs to produce COVID-19 test The scientists also made the pro- focus from the origins of life to kits. Samantha Mascuch, a postdoc tein DNA polymerase (the enzyme COVID-19 test kit production. “Like studying chemical ecology, and Sara that amplifies the pieces of the viral many academic scientists, we had Fahkretaha–Aval, a fifth-year grad genome) by feeding bacteria the DNA useful expertise and resources and an student studying the origins of life, instructions for making that protein. intense desire to contribute,” Williams are co–first authors of the paper. The bacteria act as little factories, said. Mascuch said working on coronavirus turning the DNA into a functional Seeing that reagents for RT-PCR was not only an honor but an ethical enzyme that is purified and used in kits were in short supply, Williams imperative. “We’re scientists,” she the COVID-19 test kit. The team at gathered a team to design a protocol said. “Certainly public money has Georgia Tech tried many types of mo- for academic labs to produce kits gone into training us, and I think it’s lecular probes and DNA polymerases cheaply. “Once we launched, we were important for us to use what skills we before they found the most accurate nearly swamped by volunteers with all have to give back.” and efficient combination. kinds of amazing skill sets,” he said. The protocol reduces costs so that Beyond being involved in exempla- The team grew to more than 30 even labs with small budgets can ry scientific research, Fahkretaha–Aval scientists from diverse backgrounds, contribute. In RT-PCR tests, pieces of is proud to have made a global re- including undergraduate and graduate the viral genome are recognized with source. “We wanted to do something students, postdoctoral fellows, labora- molecular probes and amplified by an for the whole world,” she said. “The tory technicians, and professors. Social enzyme. The new protocol instructs U.S. didn’t have enough test kits, distancing rules made it difficult to scientists how to make the molecular which made me think about other, train recruits, but the researchers man- probes and enzymes in-house instead poorer countries with bad economies. aged, sometimes using video calls to of having to buy them, drastically Or countries like my own, Iran, that demonstrate how to use instruments cutting costs. are under sanction or embargo.” or perform techniques. The molecular probes that bind To determine if the kits could The project culminated in a paper and recognize the COVID-19 genome detect SARS CoV-2, the virus that published in the Journal of Biologi- are short fluorescent pieces of DNA. causes COVID-19, on surfaces, a cal Chemistry that provides step- DNA is composed of nucleotides subgroup of researchers took samples by-step instructions for academic called adenine, guanine, thymine and around the Georgia Tech campus at
18 ASBMB TODAY DECEMBER 2020 JOURNAL NEWS COURTESY OF SARA FAHKRETAHA–AVAL
The more than 30 Georgia Tech scientists who developed a protocol to make COVID-19 test kits from scratch, top to bottom and left to right. Row 1: Samantha Mascuch, Sara Fakhretaha–Aval, Jessica Bowman, Minh Thu Ma, Gwendell Thomas, Bettina Bommarius, Chieri Ito. Row 2: Liangjun Zhao, Gary Newnam, Kavita Matange, Hem Thapa, Brett Barlow, Rebecca Donegan, Nguyet Nguyen. Row 3: Emily Saccuzzo, Chiamaka Obianyor, Suneesh Karunakaran, Pamela Pollet, Brooke Rothschild–Mancinelli, Santi Mestre–Fos, Rebecca Guth–Metzler. Row 4: Anton Bryksin, Anton Petrov, Mallory Hazell, Carolyn Ibberson, Petar Penev, Robert Mannino, Wilbur Lam. Row 5: Andrés García, Julia Kubanek, Vinayak Agarwal, Nicholas Hud, Jennifer Glass, Loren Williams, and Raquel Lieberman.
stores, gas stations and even other the quality and efficacy of the kits. produce new tests, treatments, and labs. After the paper was published, Labs can produce test kits that meet vaccines.” collaborators at the University of these standards more easily by follow- DOI: 10.1074/jbc.RA120.015434 Georgia tested the kit’s ability to ing the Georgia Tech protocol. detect the virus in patient samples. By This protocol also arms communi- Lisa Nicole Learman every metric tested, the homemade ties worldwide to respond to future ([email protected]) is a Ph.D. kits work as well as, if not better than, shortages. Fahkretaha–Aval believes candidate studying molecular commercially available kits. more labs need to make resources neuroscience at Johns Hopkins University School of Medicine. Academic labs need an emergency for combatting COVID-19 publicly Follow her on Twitter use authorization, or EUA, to pro- available. “I hope they share the infor- @LearmanLisa. duce kits that can be distributed to lo- mation like we did,” she said. “I hope cal testing centers; the Food and Drug that all of the scientists and compa- Administration requires data showing nies share their information after they
DECEMBER 2020 ASBMB TODAY 19 JOURNAL NEWS
From the journals By Himanshi Bhatia, Amrita Mandal & Anand Rao
We offer summaries of recent protein as possibly involved in the folded proteins commonly found in papers in the Journal of Biological transport process. These findings are hepatocytes of patients with liver dis- Chemistry, the Journal of Lipid expected to pave the way for better ease such as hepatocellular carcinoma, Research and Molecular & Cellular understanding of CVDs and other hepatitis B and C, and alcoholic and Proteomics. disorders of cholesterol metabolism. nonalcoholic steatohepatitis. Abnor- DOI: 10.1194/jlr.RA120000635 mal protein aggregation, a common A novel cholesterol hallmark of several neurodegenerative New tools to study diseases, leads to the transcription trafficking pathway in blood aminoacyl-tRNAsynthetases factor nuclear factor–kappa B, or NF- Cardiovascular diseases, or CVDs, kB, activation. This activation initi- account for 31% of all global deaths. Aminoacyl-tRNA synthetases, or ates an inflammatory cascade. Howev- They are characterized by underlying aaRSs, are enzymes that polymer- er, researchers have not yet identified causes such as atherosclerosis involv- ize amino acids to synthesize tRNA, the mechanistic link between protein ing anomalies in cholesterol transport and they have a well-known role as aggregation and NF-kB activation. and deposition. Therapies such as housekeeping proteins. However, In hepatocytes, the inhibitor of lipid-lowering drugs have reduced the researchers have lacked the tools to NF-kB, or IkB, family of proteins risk of CVDs but have not eliminated appreciate the extent of their biologi- inhibits NF-kB activation by masking them, indicating the existence of cal functions. its nuclear localization signal, leading additional factors that influence lipid In a recent paper published in to cytoplasmic retention of NF-kB in metabolic pathways and contribute to the Journal of Biological Chemis- an inactive state. In a recent article development of CVDs. try, Charlotta Preger of Karolinska published in the journal Molecular In a multi-institutional study University Hospital and collaborators & Cellular Proteomics, Yi Liu at the published recently in the Journal of created high-affinity antibodies for 13 University of California, San Fran- Lipid Research, Ryunosuke Ohkawa cytoplasmic and one mitochondrial cisco, and an international team of from Tokyo Medical and Dental aaRS. The authors produced selected researchers write that they’ve found University and colleagues describe domains of these proteins in E. coli, induction of MDB production leads a unique role for red blood cells, or which they used as antigens to yield to sequestration of two proteins, IkBα RBCs, in regulating cholesterol trans- large sets of antibodies that were and IkBβ, into insoluble aggregates in port. This may help researchers design validated through binding assays. the cytoplasm. As a result, NF-kB can more effective treatments. Immunoprecipitation and mass spec- travel freely to the nucleus and initiate In this study, incubation of plasma trometry verified the antibodies’ abil- an inflammatory cascade. Using state- with RBCs resulted in a time-de- ity to capture their target proteins. of-the-art proteomics analysis, the pendent increase in serum/plasma These sequences of the proteins are researchers also identified 10 proteins, cholesterol levels. Further lipoprotein freely available to all, and the authors including nucleoporins Nup153 and analysis demonstrated cholesterol believe their work will help define the Nup358/RanBP2, in these aggregates, efflux to high-density lipoproteins and noncanonical roles of aaRSs in health which interact with IkBα upon MDB influx from low-density lipoproteins and disease. induction and prevent its nuclear in a dose- and temperature-dependent DOI: 10.1074/jbc.RA120.012893 entry and its consequent termination manner with no transport to lipopro- of NF-kB-activation. These findings tein-depleted plasma. Using RNAi A key to inflammation provide new therapeutic targets to machinery and bioinformatic analysis, in liver disease study protein aggregation related to the researchers identified ATP-bind- inflammation in liver disease and pos- ing cassettes ABCA7 and ABCG5, Mallory–Denk bodies, or MDBs, sibly in neurodegenerative diseases. lipoprotein lipase and translocator are cytoplasmic aggregates of mis- DOI: 10.1074/mcp.RA120.002316
20 ASBMB TODAY DECEMBER 2020 JOURNAL NEWS
Vascular proteomics in citrus disease Huanglongbing, or HLB, is a devastating citrus plant disease that causes huge economic losses to the citrus industry worldwide. The causal bacterium, Candidatus Liberibacter asiaticus, or CLas, is spread by Diaphorina citri, a sap-sucking citrus plant bug, and ends up in the plant’s vascular system. ISTOCKPHOTO.COM Fruits affected by the disease are greener, smaller than nor- mal, and overall bitter in taste. Once a tree is infected with HLB, it eventually dies. Previous studies have looked at host responses in leaf, root and fruit, but scientists have lacked information regarding the proteomics of the vascular system where the bacterium resides. To address this issue, Jessica Y. Franco and a group of researchers at the University of California, Davis, and in Texas performed proteomic analysis of plant bark samples from the sweet orange variety Washington navel inoculated with CLas. The analysis revealed upregulation of proteins important for pathogen recognition and plant defense response. The researchers also compared and found variabil- ity in peroxidase enzymatic activity among different citrus species. Serine protease and hydrolase activity also changed dynamically during CLas infection. These findings indicate Huanglongbing disease, shown in an orange, is caused by bacteria spread genetics and environmental conditions influence the host by a citrus plant bug. defense response. Overall, this study, published recently in the journal Molecular & Cellular Proteomics, showed that the Washing- ton navel orange had a 51% change in global proteome during CLas infection. Future investigation to assess plant host response in different genotype and environmental conditions will provide a better understanding of the disease. DOI: 10.1074/mcp.RA120.002075
New work casts doubt in cancer cells, but Martin Baker of implications for the study of this key on antibody’s role the University of Pennsylvania and GTPase in cancer, chiefly because collaborators stumbled across incon- many cancer cell lines with charac- in cancer studies sistencies that prompted them to con- teristic mesenchymal attributes show Scientific researchers make progress duct a deeper characterization of this upregulation of vimentin that coin- by standing on the shoulders of those antibody. Using prostate and pan- cides with high basal Rac1-GTP levels who came before them. Through an creatic cancer models known to have when measured biochemically. This often arduous process, they test and high basal Rac1-GTP levels, they creates a misleading correlation that retest their own work before submit- demonstrated that the oft-used Rac1 could steer investigators toward inac- ting their results to their peers to antibody does not, in fact, recognize curate conclusions and derail efforts to be evaluated. Cancer research is no Rac1 but rather detects the filament develop Rac1-targeted therapeutics. exception to this model. protein vimentin. Cell lines that were DOI: 10.1074/jbc.RA120.013919 Rac1, a small GTPase involved in devoid of Rac1 showed strong signals cytoskeleton reorganization and cell when using this antibody, and these A lipid metabolite regulates motility, is elevated in several aggres- signals disappeared when vimentin sive cancers. Studies have relied on a was knocked out. neuronal firing conformation-sensitive antibody for The researchers published their Lipid-signaling molecules regu- the detection of GTP-bound Rac1 — findings in the Journal of Biologi- late neuronal processes such as fear, known as Rac1-GTP — activation cal Chemistry. The work has major anxiety, appetite, memory and pain.
DECEMBER 2020 ASBMB TODAY 21 JOURNAL NEWS
Master regulator governs color production in yeast, fungi Sterol regulatory element-binding proteins, or SREBPs, sense the intracellular lipid environment to regulate expression of key metabolism-associated genes and maintain lipid homeostasis in mammals. These functions are primarily conserved across species; in yeast and fungi, additional pathways are controlled by Sre1, the SREBP
MELISSA GÓMEZ-RÍOS homolog, with roles ranging from fungal pathogenesis to growth under hypoxic conditions. Though the roles are conserved, little is known about the mechanism of Sre1 in yeast. Previous research suggests a link between production of ergosterol, the main sterol component of the fungal cell membrane, and carotenoids, the color-pro- ducing compounds in these organisms. To gain greater understanding, authors of a recent study in the Journal of Lipid Research focused their efforts on the yeast Xanthophyllomyces dendrorhous, a natural producer of the carotenoid astaxanthin. Astaxanthin is both a coloring compound and an antioxidant, which lends com- mercial significance to this study. Melissa Gómez and colleagues from the Universi- dad de Chile performed comparative RNA- This photo shows the color variations in four strains from X. dendrorhous seeded on sequencing of modified X. dendrorhous an agar plate. strains to identify Sre1-dependent genes. They also used chromatin immunoprecipi- tation combined with lambda exonuclease digestion, or ChIP-exo, to gain further insight into Sre1 target genes. The researchers observed Sre1-binding motif in the promoter region of ergosterol biosynthesis-associated genes, including genes from the mevalonate, or MVA, pathway. They also identified two genes linked to caro- tenogenesis, crtE and crtR, as Sre1 target genes. Of these, crtR encodes a cytochrome P450 reductase, indicating the involvement of Sre1 in the biosynthesis of sterols and carotenoids. They found that Sre1 activates the expres- sion of sterol-biosynthesis and MVA pathways and hence regulates carotenoid production in yeast. These findings may benefit future studies focusing on commercially relevant compounds from yeast and fungi. DOI: 10.1194/jlr.RA120000975
Docosahexaenoylethanolamide, or international team addressed this gap (microwave versus carbon dioxide– DHEA, a type of lipid signaling by chemically synthesizing THEA induced ischemia). Lower THEA molecule, is dependent on peroxi- to use as a reference standard for levels were observed in wild-type some proliferator-activated receptor, functional analysis of naturally oc- mice and the microwave-only or PPAR, for its downstream neuro- curring THEA in biological samples. group. PPAR did not seem to play a nal functions. However, tetracosa- Euthanasia of wild-type mice and role in THEA-dependent signaling. hexaenoylethanolamide, or THEA, mice deficient in fatty acid amide However, THEA exposure signifi- has not been characterized. hydrolase, or FAAH, resulted in cantly increased firing from medium In a study published in the THEA accumulation in whole-brain spiny neurons of the nucleus accum- Journal of Lipid Research, Lin samples that depended on the mouse bens core. The findings from this Lin and Adam H. Metherel from genotype (wild-type versus FAAH- the University of Toronto and an deficient) and type of euthanasia CONTINUED ON PAGE 24
22 ASBMB TODAY DECEMBER 2020 JOURNAL NEWS
Trimming cilia down to size
Cilia are hairlike organelles protruding from the surface of eukaryotic cells. The two types of cilia are motile and non-motile, and their structure and function can vary depending on the cell type. In the case of airway epithelial cells, tufts of motile cilia beat in concert to drive the directional flow of fluids, clearing dirt, mucus and debris from the respiratory tract. Abnormalities in the length or function of these organelles can lead to multisystem disorders known as ciliopathies, such as the hereditary respiratory disorder primary ciliary dyski- nesia. While treatment options are limited for ciliopathies, uncovering the mechanisms that regulate motile cilia growth and beating could open avenues for new therapies. Kavisha Arora and colleagues at Cincinnati Children’s Hospital Medical Center discovered that autophagy, a controlled mechanism for cellular degradation, regulates motile cilia length. They did so by investigating the
link between the signaling media- EVA MUTUNGA & KATE KLEIN/UNIVERSITY OF THE DISTRICT COLUMBIA & NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY tor adenylate cyclase 6, or AC6, and kinesin Kif19a, a dual-func- tion molecular motor protein that moves along microtubules and depolymerizes them. Using mice genetically modified to specifically lack AC6 only in epithelial cells, the researchers showed that AC6 knockout airway epithelial cells have longer cilia than cells from mice that were not modified to lose AC6 and that this was due to decreased Kif19a protein levels in the cilia. Finally, to learn how modu- lation of this novel pathway translates into changes in cilia growth and function, the authors constructed functional rescue experiments using cultured tracheal cells in combination with pharmacological inhibition or activation of AMPK activity. This approach showed that activation of AMPK caused downregulation of Kif19a and longer cilia, which compromised cilia function. These findings, published in the Journal of Biological Chem- istry, provide new insights into fundamental cilia biology and may lead to new treatments for ciliopathies. This image shows cells lining a mouse airway. The cells shown in gray secrete mucus, which DOI: 10.1074/jbc.RA120.013703 traps inhaled particles. The colored cells sweep the mucus layer out of the lungs using cilia.
DECEMBER 2020 ASBMB TODAY 23 JOURNAL NEWS
CONTINUED FROM PAGE 22 geting the tumor microenvironment. informatic studies, they found several DOI: 10.1074/jbc.RA120.013820 important and previously unknown study present a novel lipid signaling modulators of mGluR signaling that molecule that regulates neuronal A proteomics study provide a rich resource for future excitability in the mouse brain. studies. Most notably, they found that DOI: 10.1194/jlr.RA120001024 of mGluR signaling AMPAR internalization was mediated The metabotropic glutamate recep- by intersectin-1, an adaptor protein Alternative splicing tors, or mGluRs, are G protein–cou- involved in endocytic trafficking. affects malignancy pled receptors important for synaptic DOI: 10.1074/mcp.RA120.002199 transmission and neuronal excitability. The tumor protein p53 fam- Activation of mGluR signaling is Preventing infections ily is composed of three members: implicated in behavior, learning and p53, p63 and p73. In response to memory. Its disruption is associated around prosthetics DNA damage, p73 interacts with with neurological diseases such as Staphylococcus epidermidis, a yes-associated protein 1, or YAP1, a autism spectrum disorder and fragile Gram-positive bacterium that fre- transcriptional coactivator, and at- X syndrome. quently colonizes on human skin, tenuates apoptosis. Researchers know Group I mGluRs (mGluR1 and can cause infections around pros- that YAP1 can associate with the mGluR5) are well known for induc- thetic implants. S. epidermidis forms pro-oncogenic phosphatase known ing long-term depression, or LTD, amyloidlike fibrils composed of the as Src homology region 2 domain- which involves an acute wave of new protein Aap to create a biofilm that containing phosphatase-2, or SHP2. protein synthesis. These newly syn- bolsters its resistance to host defenses However, researchers have not identi- thesized LTD proteins are important and antibiotics. fied the drivers of the pro-oncogenic for endocytosis or internalization of In a recent paper published in the effects of their interaction. the surface alpha-amino-3-hydroxy- Journal of Biological Chemistry, Al- Chi Ben, Xiaojing Wu and col- 5-methyl-4-isoxazolepropionic acid exander Yarawsky and Andrew Herr leagues at the University of Tokyo receptors, or AMPARs. However, of the University of Cincinnati Col- investigated the mechanisms un- researchers have not yet identified the lege of Medicine explored how bio- derpinning the association between complete molecular signature down- films are formed. Using analytical ul- YAP1 and SHP2. Using experimental stream of mGluR signal activation. tracentrifugation, circular dichroism, paradigms in cell culture and in ani- In a recent study published in dynamic light scattering and linkage mals, the team found that pro-on- the journal Molecular & Cellular studies, the authors showed that a cogenic YAP1 activities are inversely Proteomics, Charlotte AGH van pared-down biologically relevant Aap- regulated by alternative splicing and Gelder, Renske Penning and a team of like construct called Brpt1.5 forms that certain splicing isoforms confer researchers in the Netherlands report a zinc ion–induced tetramer needed greater tumorgenicity than others. that they have found novel regulators to produce the amyloids required The researchers recently published of the mGluR signaling pathway. The for biofilm formation. Their results their results in the Journal of Biolog- team first stimulated the cultured provide new avenues for potential ical Chemistry, demonstrating how hippocampal neurons with the agonist therapeutic targeting of staphylococ- abnormal splicing may exacerbate (S)-3,5-dihydroxyphenylglycin to cal biofilms to reduce infections after cancer malignancy. The work could induce mGluR activation. Next, using prosthetics are implanted. lead to novel cancer therapeutics tar- high-resolution proteomics and bio- DOI: 10.1074/jbc.RA120.013936
Himanshi Bhatia (himanshi.b@ Amrita Mandal Anand Rao ([email protected]) is gmail.com) is a postdoc- ([email protected]) an ASBMB science communica- toral research associate at the is a postdoctoral fellow at the tor. Follow him on Twitter Washington University in St. National Institutes of Health. She @AnandRaoPhD. Louis and is passionate about earned her Ph.D. in molecular science communication. Follow biology at Cincinnati Children’s her on Twitter @Himanshi16b. Hospital in Ohio.
24 ASBMB TODAY DECEMBER 2020 ASBMB Journals will be fully open access in 2021.
Journal of Biological Chemistry Molecular & Cellular Proteomics Journal of Lipid Research
The American Society for Biochemistry and Molecular Biology’s three journals will be open access beginning in January.
asbmb.org/journals-news/open-access
DECEMBER 2020 ASBMB TODAY 25 The cellular conundrums of hepatitis C
26 ASBMB TODAY DECEMBER 2020 FEATURE
Charles Rice, who shared the 2020 Nobel Prize in physiology or medicine, has spent his career unraveling the genomic secrets of flaviviruses and other positive-strand RNA viruses By John Arnst
epatitis C is a rarity among the viruses that infect humans on a global An estimated 71 million people scale. Although an effective vaccine still is being developed for it, prop- worldwide are chronically Herly administered antivirals can eliminate the virus in 95% of the people who are infected with it. infected with hepatitis C virus. But it hasn’t been an easy nut to crack. When the virus was isolated in 1989, scientists ran into repeated dead ends as they tried to get it to replicate in cell Without treatment, a significant culture. The journey to develop an effective system in which to grow and study number of those who are HCV involved hundreds of scientists and took more than 15 years. In October, Charles Rice at The Rockefeller University, along with Harvey J. chronically infected will develop Alter at the National Institutes of Health and Michael Houghton at the Univer- sity of Alberta, won the Nobel Prize in physiology or medicine for their seminal cirrhosis or liver cancer. discoveries leading to the identification of the hepatitis C virus. “It was a huge surprise to me, and a shock, and a very humbling experience,” said Rice. “When you think about the many people that have been involved in this success story, it’s something that has spanned decades and involved thou- sands of dedicated scientists and clinicians to really get to where we are today.”
Epidemic jaundice COURTESY OF CHARLES RICE The Hippocratic physicians are credited with the first descriptions of contagious jaundice in the fifth century B.C. The condition, the hallmarks of which are yellowing of the skin and the whites of the eyes and dark urine, occurs when liver inflammation or a blocked bile duct allows bilirubin to build up in the blood. “The connection made between the liver and jaundice was remark- able, bearing in mind that the Hippocratic physicians had not performed dissections and that Charles Rice, who won this year’s Nobel Prize in physiology or medicine with Harvey Alter and Michael their medical views were based on Houghton, also won the Lasker Award in 2016 with Ralf Bartenshlager and Michael Sofia for developing a observation,” Niki Papavramidou, system to study the replication of the virus that causes hepatitis C.
DECEMBER 2020 ASBMB TODAY 27 FEATURE
Elizabeth Fee and Helen Christopou- “non-A, non-B” hepatitis and now The ABCDEs of hepatitis lou–Aletra wrote in the Journal of known as hepatitis C, became a prior- Gastrointestinal Surgery in 2007. ity for Michael Houghton, who was B While overconsumption of alcohol, Epidemic jaundice was recorded in working for the pharmaceutical firm environmental toxins and autoimmune the 17th and 18th centuries. Tens of Chiron at the time. disease play significant roles in global thousands of Union soldiers during In 1989, Houghton and his col- incidence of liver inflammation, or hepa- the American Civil War were sick- leagues Qui-Lim Choo and George titis, viral infections cause the majority ened. Kuo isolated a near-complete genetic of cases. D By the 1940s, scientists had begun sequence of HCV, which allowed The Hippocratic physicians in the fifth century B.C. identified five types to differentiate between hepatitis A other scientists to develop blood-based of jaundice based upon the color of and B by comparing their incubation screening tests for it. A patients’ skin, urine and feces and other times. That same year, Charles Rice, then symptoms. By coincidence,A there are five During World War II, hundreds of at the Washington University School hepatitis-causing viruses. thousands of American and European of Medicine in St. Louis, developed Hepatitis A, B, C and E viruses all troops contracted viral hepatitis. In the first infectious clone of yellow cause liver inflammation, but none of the one case, upward of 330,000 U.S. ser- fever virus, the prototype flavivirus viruses shares close lineage. vice members contracted HBV after in the family Flaviviridae, which also Hepatitis A and E are transmitted by being given a yellow fever vaccination includes the mosquito-borne dengue, E contaminated food or water and cause that contained contaminated human Zika and West Nile viruses. acute disease. E blood serum. Not long after, Rice received a call BHepatitis B and C, as well as hepatitis D, which can propagate only in the Medical anthropologist Baruch from Stephen Feinstone at the U.S. presence of hepatitis B, are chronic “Barry” Blumberg discovered HBV Food and Drug Administration, who blood-borne pathogens that spread serendipitously in 1967. He was in- wanted him to retool his work to through intravenous drug use and blood terested in how inherited traits make tackle this new flaviviruslike agent — C transfusions. people more or less susceptible to HCV. Together, blood-borne D hepatitis disease and for his studies traveled the viruses, which result in cirrhosis and liver globe collecting blood samples from Rice’s flaviviral cancer, cause more than 1 million deaths remote populations. each year. He found a surface antigen for investigations hepatitis B in the blood of an Indig- After graduating with a bachelor’s enous Australian, which led to the degree in zoology from the University identification of the virus and its role of California, Davis, in 1974, Rice be- in causing acute and chronic hepatitis gan graduate school at the California and liver cancer. Institute of Technology. He initially In 1976, Blumberg, along with D. planned to continue his undergradu- ate research in developmental biology, Hepatitis C virus, pictured here with a scale bar of Carleton Gajdusek, won the Nobel 50 nanometers, currently infects approximately Prize for physiology or medicine for but his first lab placement was with 71 million people worldwide. their work on the virus. Blumberg’s virologist James H. Strauss Jr.
CHARLES RICE/THE ROCKEFELLER UNIVERSITY birthday, July 28, was adopted as “I started working in the Strauss World Hepatitis Day in 2008. lab, which was really the only active virology lab at Caltech,” Rice said. “And I really enjoyed that, so I just Not A or B, but C stayed there.” In the early 1970s, National Near the end of his doctoral work, Institutes of Health physician Harvey completed in 1981, Rice began study- J. Alter was investigating hepatitis ing the mosquito-borne yellow fever in patients who had received blood virus, after which both the genus transfusions but had tested negative Flavivirus and family Flaviviridae are for both the A and B viruses. named. He continued his research as a The new illness, then known as postdoctoral fellow in Strauss’ lab for
28 ASBMB TODAY DECEMBER 2020 FEATURE
the next four years. and worked closely with Alexander COURTESY OF ARASH GRAKOUI After briefly working at the “Sasha” Kolykhalov. Australian National University with “After the Soviet Union collapsed, Lynn Dalgarno, who had co-discov- a lot of very excellent — like, ered with John Shine in 1973 the literally, some of the top Russian Shine–Dalgarno sequence involved virologists in mRNA translation initiation, Rice — just took a faculty position at WUSTL in came and 1986. There, he continued to work worked in with yellow fever virus. Charlie’s “At Caltech, we’d already deter- lab more mined the genome structure of the or less as virus and had some ideas about what postdocs,” the expression strategy might be for BRETT LINDENBACH said the viral proteins,” Rice said. “But Linden- at Wash U, I was actually trying to bach, who also did his second build an infectious clone for yellow postdoctoral fellowship with Rice at fever that would allow us to do more The Rockefeller University. “Most of directed genetic manipulations on this them came from Novosibirsk, which virus to understand more about how is where the Soviet Union did its it works.” bioweapons virus research.” When Kolykhalov and Rice began Arash Grakoui, left, who was the first lab tech that Rice was building consensus clones, full- Charlie Rice hired in 1987 when he was starting setting up length complementary DNAs his lab at WUSTL, has gone on several excursions his lab in (called cDNAs for short) of HCV to Wyoming over the years with Rice, right, whom early 1987, that are cloned within bacterial he describes as an avid outdoorsman. the first plasmids, but the clones were never person functional in cell culture or in chim- he hired panzees, the only other animal the ARASH GRAKOUI was Arash virus is known to infect, Linden- Grakoui, bach said. This led them to believe who had just earned an undergraduate that they might be dealing with an degree and was looking for employ- incomplete genome. ment as a lab tech. “Charlie and Sasha set out to try “It was Charlie and me, and we and discover what the real 5' and had a bench, sitting across from 3' ends of the viral genome were,” one another. And soon there was a Lindenbach said. “They confirmed graduate student, and then a postdoc that the 5' end was indeed correct, as well,” said Grakoui, now a profes- but then they discovered this big sor of medicine at Emory University. piece of the 3' end that had been “Right off the bat, he trained me as missing.” a student or postdoc in the lab and Kolykhalov, Rice and Feinstone let me have a lot of freedom to be reported their findings about a creative.” highly conserved sequence element The next few years also saw a spate at the 3' end of the HCV genome of more unusual hires, and Rice’s lab in 1996 in the Journal of Virology. began working with HCV. Brett Lin- The next year, Rice reconstructed denbach, a professor of microbiology a full-length consensus clone, a at Yale University, was a graduate stu- single cDNA clone representing the dent in Rice’s lab through the 1990s average of variants within the viral
DECEMBER 2020 ASBMB TODAY 29 FEATURE CENTERS FOR DISEASE CONTROL AND PREVENTION population, but still had no system to Lohmann figured out how to select test it in. for a variant of the virus to replicate Despite the researchers’ best efforts, in HuH7 cells originally derived the variant refused to replicate in any from a cancerous tumor in human established cell lines. So Feinstone liver through use of a subgenomic injected the viral variant into the replicon system. livers of two chimps. (Author’s note: “What they did was to chop out In 2015, the National Institutes of a chunk of the genome that encoded Health announced that it would no what we believed to be the structur- longer support biomedical research al proteins of the virus, the glyco- involving chimpanzees.) proteins and the capsid protein, and “This was a Hail Mary sort replace that with a drug-selectable of experiment, because this is a marker,” Rice said. 10,000-base-pair-long RNA,” Rice That marker was a neomycin said. “And if you’re just injecting it gene that confers resistance to into an organ in vivo and hoping that the drug G418, to which human somehow it gets inside of a cell so it cells are sensitive. By exposing the can be translated by that machinery, hepatic cells to G418, the cells that you’re hoping to get lucky.” did not support the HCV replicon Rice, Feinstone and their co-au- and take up the drug resistance thors did get lucky: The virus caused gene were wiped out, leaving only changes in blood and pathology HCV-laden cells for the researchers resembling those seen in humans with to pore over. hepatitis C, providing direct evidence “If you’re looking for a needle in In 1998, the Centers for Disease Control and that HCV was responsible for the a haystack, you need a big magnet. Prevention put out educational pamphlets transfusion-mediated hepatitis. And that’s what this was,” Linden- about testing and diagnoses for hepatitis C Their 1997 paper, published in the bach said. virus, with which nearly 4 million Americans journal Science, noted that the scien- Rice and his colleagues then were then infected. tists had fulfilled Koch’s postulates found that variants of HCV in the on a molecular level: An infectious subgenomic replicon system har- organism must be present during each bored mutations that were adaptive case of a disease and must able to be to their environment. When those isolated and purified, and the organ- mutations then were engineered ism must cause the disease when a into new replicons, the researchers new host is infected with it. found that they could increase the “I recall pointing out that this efficiency of the system more than helps to prove that HCV is the 10,000-fold. causative agent of hepatitis C, because Another advance came in 2002 it fulfills sort of a molecular form of when Keril Blight, one of Rice’s Koch’s postulates,” Lindenbach said. postdocs, helped cure cells of “And Charlie thought that was a great replicons to see if there might be a idea and wrote that into the paper.” selection for more HCV replicon- permissive cellular environments. Hepatic breakthrough The increased permissiveness of one of the cured cell lines allowed the re- While the researchers lacked a searchers to detect HCV RNA and way to study the virus in cell cul- antigens early after RNA transfec- ture, a model arrived in 1999. Ralf tion, which eliminated the need for Bartenschlager, a professor at the selection of replication-positive cells. University of Mainz, and Volker The final breakthroughs for grow-
30 ASBMB TODAY DECEMBER 2020 FEATURE COURTESY OF ARASH GRAKOUI ing hepatitis C arrived in 2005, when a team that included Japanese virolo- gist Takaji Wakita and Bartenschlager found that a rare isolate of HCV from a patient in Japan with acute fulmi- nant disease was able to undergo its entire life cycle in cell culture without induced mutations. At the same time, Rice’s group, including Lindenbach, described a chimeric full-length HCV genome that replicated and produced virus particles that were infectious in cell culture, and a group led by Frank Chisari at Scripps Research reported a robust HCV replication system that used the JFH-1 molecular clone and HuH-7–derived cell lines. In the years that followed, research- ers were able to develop direct-acting antivirals for hepatitis C. Until that From left, John Majors, Stan Birge, Sadie (dog), Peggy MacDonald, Claire Birge, Charles Rice, Arash point, the viral infection had been Grakoui and Holly Hanson visit Wyoming in 1995. treated with the more broadly acting antivirals pegylated interferon and the lab of immunologist Paul Allen in ribavirin, a combination that carried 1994 after seven years in Rice’s lab, to significant side effects and only boast- join him as a postdoctoral fellow. ed a 50% success rate of eliminating “Coming back as a postdoc really the virus, Rice said. enabled me to bring along all the In 2014, the FDA approved the tools that I had gathered in graduate direct-acting combination pill Har- school to tackle some of the questions voni made up of the drugs ledipasvir that we were interested in about viral and sofosbuvir, which are effective in immunology,” he said. eliminating HCV in more than 95% During their years at WUSTL, of the people who take them. Rice, an avid outdoorsman, had in- According to Craig Cameron, a troduced Grakoui to fishing through virologist at the University of North long excursions to Wyoming. Carolina at Chapel Hill, while “Charlie described to me on one HCV is able to develop resistance to of our trips that fishing is a lot like individual drugs, a combination of science: You don’t actually expect to antivirals that target different viral catch anything, but if you do, it is functions kills the virus outright. incredible,” Grakoui said. “You have “If you hit it hard enough, long done the best you can, and you just enough, you can force it to extinc- let nature takes its course.” tion,” Cameron said.
John Arnst (jarnst@asbmb. Nice catch org) is an ASBMB Today science writer. Follow him In 2001, Rice moved his lab to on Twitter @arnstjohn. Rockefeller in New York. In 2002, he convinced Grakoui, who had enrolled as a graduate student at WUSTL in
DECEMBER 2020 ASBMB TODAY 31 FEATURE
FROM bacterial immunity TO scientific revolution
32 ASBMB TODAY DECEMBER 2020 FEATURE
CRISPR’s sprint to the gold
By Laurel Oldach HALLBAUER & FIORETTI, BRAUNSCHWEIG, GERMANY The most important hat can I tell you about molecular biology discovery CRISPR that you haven’t Wheard before? of the 21st century The technology has been the is only 8 years old. subject of countless journal clubs and chalk talks; it has exploded in citation count and triggered a wave of creative applications that has yet to crest. It has swept through biology labs, en- abling researchers to modify genomes Emmanuelle Charpentier is the founding from Aspergillus to zebra mussel. director of the Max Planck Unit for the Science No matter how groundbreaking of Pathogens in and a professor at the Humboldt a discovery is, by the time it wins University in Berlin. the Nobel Prize, the dust usually has settled. The finding or technique A strange season matures, becoming another slab in the to celebrate foundations of science. CRISPR is different. Some On the day it was announced that postdocs now using the technology this year’s Nobel Prize in chemistry as a matter of course were graduate was awarded to Emmanuelle Char- students when its potential first was pentier and Jennifer Doudna for grasped. The most important mo- their joint contribution to the use of lecular biology discovery of the 21st CRISPR–Cas9 as a technology for ge- century is only 8 years old. nome editing, Charpentier remarked
INNOVATIVE GENOMICS INSTITUTE ruefully to an interviewer from the Nobel press office, “You connect to (the news), but you think it’s another person, or it’s surreal. … Now it’s real, and now I have to deal with it.” bacterial immunity A month later, Doudna told this reporter, “It’s been a whirlwind, as you can imagine. But there’s so much going on in the world right now that’s scientific revolution a bit horrifying, but also motivating for scientists.” Before the Nobel announcement on Oct. 7, Doudna was focused on Jennifer Doudna is a professor at the University pandemic response at the Innova- of California, Berkeley, and founder of San tive Genomics Institute, which she Francisco’s Innovative Genomic Institute.
DECEMBER 2020 ASBMB TODAY 33 FEATURE
COURTESY OF MEGAN HOCHSTRASSER founded in 2014 and co-leads. That A fashionable topic work includes both a clinical testing program launched in the spring, Nobel-winning duos in the bio- and a more recently announced chemical sciences often are scientists diagnostic technique for using who have spent a significant fraction CRISPR ribonucleoproteins and a of their careers working together. cell phone to detect SARS-CoV-2 Doudna and Charpentier’s col- in patient samples. laboration, in contrast, was brief “I wish we weren’t having to do and electrifying. They published just that, obviously,” Doudna said of the two research articles together — two IGI’s all-hands-on-deck pandemic articles with massive impact. response. Then she added, “I think The idea of programmable genome this is what science needs to do. As engineering began long before their Megan Hochstrasser works in education and academics, we’re not always trained CRISPR work did. Restriction outreach at the Institute for Innovative Genomics. to do this. But … we need to be enzymes, which cut DNA at specific “One of the things that sets Jennifer apart from nimble, and we need to be able to sequences, first were described in the people is that she really sees the value in com- ask ourselves: How does our exper- 1960s. The discovery led research- municating things well,” Hochstrasser said. tise apply in this moment?” ers to reason that if they could alter Megan Hochstrasser earned her a restriction enzyme’s cut site, they Ph.D. in the Doudna lab working could modify DNA sequences with on CRISPR and now does outreach exquisite precision. For a time in the and education at the IGI, which she early 2000s, researchers interested in views as Doudna’s effort “to make programmable DNA cutting focused sure CRISPR leaves the lab and on two classes of proteins called reaches the real world — and on zinc finger nucleases and transcrip- top of that, make sure that the way tion activatorlike effector nucleases, it reaches the world is positive.” or TALENs. Both are made up of Hochstrasser has witnessed the modular DNA-binding protein do- evolution of CRISPR from when mains, which can be daisy chained to she was a grad student, when she recognize a given sequence. But both got “to see a technology develop proved difficult to engineer. into something wildly important, Doudna and Charpentier dem- when it started out as kind of an onstrated that a new programmable esoteric thing.” Since moving to the system for DNA cutting could be IGI, she has watched it “grow from simplified to just two components: being very tiny to starting to get one protein and one RNA. much bigger and more impactful.” Microbiologists had been aware The IGI also brings together a for some time of a curious repeating team of scientists who can pool feature in bacterial genomes called their expertise. In many cases, clustered regularly interspaced short Doudna said, “There’s no one of palindromic repeats, or CRISPR for us that has the whole package of short (see “Yogurt research, broad expertise … so we need to work applications” on page 40). In 2005, together to do something that no Spanish scientists discovered that one of us would be capable of doing the spacer sequences in between the on our own.” repeats matched up to the genes of Collaboration is exactly how viruses that infect bacteria. They pro- Doudna got into the CRISPR field posed that the system might represent in the first place. a kind of bacterial adaptive immu- nity: a way to recollect and respond to
34 ASBMB TODAY DECEMBER 2020 FEATURE
JERRY GU, JUNG-HEE LEE, VICTORIA TOKARZ & CINDY LIU / COURTESY OF BIORENDER pathogens encountered before. that occurred to many researchers. “CRISPR became a super fashion- The hypothesis of a bacterial able topic,” said Krzysztof Chylinski, immune system caught on, and a who developed an interest in CRISPR number of labs began to work on himself when he joined Charpentier’s characterizing the CRISPR system lab. He chalked up its popularity not and the CRISPR-associated, or Cas, just to the novelty of a complex adap- proteins it requires. tive immunity system in an organism Charpentier’s microbiology lab no one had expected to contain one in the Max Perutz Laboratories at but also to the possible applications the University of Vienna was one of
DECEMBER 2020 ASBMB TODAY 35 FEATURE UNIVERSITY OF ZURICH them. The lab, which Charpentier guided by just one RNA, Charpen- had founded in 2002, worked on vir- tier’s lab had realized that S. pyogenes ulence factors in various pathogenic requires two RNAs. Soon they would bacteria, including an RNA-regulated find that the system also involved only system in Streptococcus pyogenes. A one effector protein, called Cas9. bioinformatics screen they conducted The simplicity of the S. pyogenes in 2006 revealed that pyogenes too system was tantalizing. Chylinski had a collection of clustered regularly explained, “If in one system, you have interspaced repeats. They became like six proteins that are doing some- interested in a noncoding RNA near thing, and in the other there is one, it Martin Jinek was a postdoctoral researcher in the CRISPR locus that they thought must be one hell of a special protein.” Doudna’s lab and was co-first author on the 2012 might regulate the CRISPR system’s paper describing the mechanism of Cas9. activity.
COURTESY OF KRZYSZTOF CHYLINSKI The same type of scientist Around the same time, Doudna, a structural biologist who had been Doudna and Charpentier met at focused on RNA interference in eu- a CRISPR conference in San Juan, karyotic cells, learned about CRISPR Puerto Rico, in 2011 when the through a conversation with Jillian CRISPR field was still small enough Banfield, a colleague at the University to fit into a single room. They hit it of California, Berkeley. Intrigued off right away, both sharing a love by the similarities between eukary- of hard problems and careful inves- otic RNAi and the CRISPR system, tigation. Charpentier told a Nobel Doudna started investigating the interviewer, “We are the same type of Krzysztof Chylinski was a graduate student in structure and activity of Cas enzymes scientist, who want to see the details Emmanuelle Charpentier’s lab and was co-first in Pseudomonas aeruginosa and, with of the data.” author on the 2012 paper describing the mecha- collaborator Eva Nogales, published The two labs came together for an nism of Cas9. in 2011 a cryogenic electron micros- often-described transcontinental and copy structure of the E. coli CRISPR transoceanic collaboration. Though it effector, a involved just two labs, it took place in complex three locations: Berkeley, Vienna, and with many Umeå — a city in Sweden to which protein Charpentier was moving her lab. Soon compo- Chylinski and Martin Jinek, a postdoc nents. in the Doudna lab, were hard at work Also using purified Cas9 protein and tracr in 2011, and CRISPR RNAs to understand Chylinski EVA NOGALES how Cas9 cuts target DNA. was second The work went smoothly. None of author on a report from Charpentier’s the researchers recalled any extraordi- lab. They found that the noncoding nary roadblocks. RNA they had taken an interest in, “If it would be easy, everything dubbed the transactivating CRISPR would have been discovered already,” or tracrRNA, had to be present for Chylinski said. But in this project, the S. pyogenes CRISPR RNAs to the hurdles that arose were “just, you mature into an active form. know, regular troubleshooting, and There are some important dif- let’s move forward.” ferences between the E. coli and S. The results, too, were clear. “Some- pyogenes CRISPR systems. Whereas times you work on systems, and it E. coli and a majority of other bacte- takes a long time to see what you ria have systems with many proteins would like to see — or the result is
36 ASBMB TODAY DECEMBER 2020 FEATURE INNOVATIVE GENOMICS INSTITUTE not black and white, it’s light gray or dark gray,” Charpentier explained to a Nobel interviewer. “Here, it was really white.” The team found that base pairing between the tracr and CRISPR RNA could lead Cas9 to cut a DNA target that matched the CRISPR RNA so long as the target DNA included a protospacer-adjacent motif nearby. They also demonstrated that a single engineered hairpin RNA could per- form the same role — in other words, they established a two-component system for genetic engineering. Because CRISPR had intrigued so many researchers, the team knew that A 3D-printed model of the structure of Cas9 they needed to publish soon to beat been published. (white) in complex with an RNA guide and DNA their competitors. “All of a sudden, tons and tons of template, based on the structure that Doudna’s “Towards the end … it became labs could afford genome engineering as a very standard thing,” Chylinski lab solved, is one of her signature tools for science kind of an around-the-clock opera- communication. tion,” Jinek said. “We took advantage said. He fielded a slew of technical of the time difference.” He would questions about the tool while finish- wake up to an email from Chylinski ing his Ph.D., and after graduation reporting on the day’s results and he took a job at a small nonprofit that would send a similar email before he provides technical services to help re- headed home. search labs implement the technology. The work was published in Science Doudna and Charpentier each in 2012. A year and a half later, they launched biotechnology companies in followed up, again in Science, with 2013: Charpentier started CRISPR a detailed structural description of Therapeutics, while Doudna (who More reading on how two years prior had started Caribou two Cas9 proteins from two bacterial CRISPR was discovered species and how each of them coordi- Biosciences based on her own lab’s CRISPR work) teamed up with Feng nated DNA and RNA. A Crack in Creation Zhang of the Broad Institute and by Jennifer Doudna with Samuel George Church from Harvard and CRISPR’s big break Sternberg MIT, along with several others, to The CRISPR field already was start Editas Medicine. Later, overlap- “The biology of CRISPR–Cas: moving fast. Once the 2012 paper on ping applications for patents on Cas9- Backward and forward” reprogramming Cas9 was published, based genome editing pulled the UC by Charpentier and colleagues in Cell it exploded. Labs around the world system and the Broad Institute into a “A day with Jennifer Doudna” picked it up rapidly. Already by the long-running, bitterly fought and well by Lisa Jarvis time of their second paper, Doudna, publicized dispute over ownership for Chemistry & Engineering News Charpentier and Nogales could cite of the rights to use CRISPR–Cas9 “The quiet revolutionary” seven major articles that had used genome editing in eukaryotic cells. by Allison Abbott for Nature CRISPR and Cas to induce double- Though it’s still unclear who will “The promise and challenge of stranded breaks in DNA, modulate win commercial rights to CRISPR– therapeutic genome editing” transcriptional activity and modify Cas9, in basic research the outcome is by Jennifer Doudna in Nature eukaryotic genomes — and those clear. “Everybody uses it,” said RNA were just the projects that already had structural biologist Joan Steitz, who
DECEMBER 2020 ASBMB TODAY 37 FEATURE
knew Doudna as a postdoc at the “For many scientists, this is a The many uses for CRISPR Unviersity of Colorado and a junior foreign area: We’re not trained to talk professor at Yale. about our work more broadly,” she The mechanistic understanding of said. “Many of us prefer to do the bacterial immune systems that Jennifer Societal implications next experiment rather than stepping Doudna and Emmanuelle Charpentier out of the lab and thinking about contributed to has engendered a huge At this year’s inaugural World how to communicate our science to explosion of creative uses for the CRISPR Day on Oct. 20 sponsored non-specialists — but I do think it’s technology. There are far too many by the CRISPR service company essential to do that.” to cover them all, but here are a few Synthego, Fyodor Urnov shared Urnov said during his World intriguing applications. Some are a story about stepping out of his CRISPR clearly translational, while others solve office at the IGI, which he co-leads Day talk, problems in basic research. Either way, with Doudna, for an espresso a “I salute the first thing that any CRISPR scientist week or two before the Nobel was Jennifer, will tell you about their field is that basic announced. personally, research can have applications no one He happened to be wearing a for taking would have predicted. Researchers have CRISPR T-shirt. The barista asked, such a clear used CRISPR technology: “Do you do that genome editing citizen–sci- thing?” FYODOR URNOV entist role,” ■ To record transcription events in a Yes, Urnov said. “In fact, I work adding living cell with reverse transcription with Jennifer Doudna.” that he hopes more scientists will take ■ As a target, in its native bacteria, for Impressed, the barista gave him inspiration from her sense of civic new antibiotics the coffee on the house. responsibility. Even before the prize, Doudna ■ To edit DNA only in cells illuminated A gifted explainer from the start, with blue light through photo-activat- and Charpentier had reached inter- Doudna drew inspiration from the ed dimerization national celebrity status, racking up famous Asilomar conference in the a series of other high-profile recog- 1970s, which established scientific ■ To knock out every gene in a cancer nitions. The pair shared a Break- guardrails around recombinant DNA. cell line one by one, finding drivers of through Prize in 2015, a Tang Prize When planning a conference to drug resistance in 2016 with CRISPR researcher discuss the implications of CRISPR ■ To alter genome architecture by Feng Zhang, a Japan Prize in 2017, technology, which took place in bringing two DNA regions together a Kavli Prize in 2018 with Lithu- Napa Valley in 2015, she invited anian CRISPR researcher Virginijus To power gene drives that can propa- two researchers who’d attended and ■ Šikšnys and a Wolf Prize earlier this gate through mosquito populations organized the original, Paul Berg and year. In the wake of their discovery, David Baltimore. ■ To generate more realistic, geneti- both have founded institutes that Many of those same researchers, cally diverse tumors in animal models they now lead: Doudna at the IGI including Doudna and Baltimore, ■ To manipulate RNA levels without and Charpentier, in 2018, at the were at the Second International altering DNA Max Planck Unit for the Science of Summit on Human Genome Editing Pathogens in Berlin. in November 2018, when Chinese Of the two, Doudna seems more researcher He Jiankui announced the comfortable stepping onto the astonishing news that he had edited global scientific stage. Both have a receptor called CCR5 out of the been involved in public conversa- genome of human embryos — and tions about the ethics of CRISPR, that edited twins recently had been but Doudna has been more focused born. The work was sloppily executed, on bringing that conversation to and the scientific rationale for altering nonscientists and has become the CCR5 was hazy; in January of this public face of the technology and its year He was sentenced to a three-year implications. prison term. Scientists around the
38 ASBMB TODAY DECEMBER 2020 FEATURE
world renewed their calls for a mora- torium on heritable editing, but He’s CRISPR vs. COVID-19 announcement already had shown the In late September, researchers from Jennifer Doudna’s lab and collaborators at the limits of such appeals. University of California, Berkeley, UC San Francisco and the Chan Zuckerberg Biohub posted a preprint introducing a method for using a CRISPR-based system to diagnose Many more CRISPR systems COVID-19 without amplifying its nucleic acids. Instead of the famous Cas9 protein, which cuts DNA at a site of complementarity with a guide RNA, this assay uses the While modification of human protein Cas13, another effector in the arsenal of bacterial CRISPR immune systems. embryos sucks up a lot of the oxygen The technique is called specific high-sensitivity enzymatic reporter unlocking, or in public conversations about genome SHERLOCK. Cas13 responds to a guide–target match by cutting the target RNA — and, editing, Urnov may have spoken for when purified, snowballing to cut every other RNA in the vicinity. It is well-suited for de- more scientists than himself when he tecting a small amount of nucleic acid. The assay has four parts: Cas13, its guide RNA, said at his World CRISPR Day talk, an RNA probe with a fluorescent moiety on one end and a quencher on the other end, holding a hand level with his eye- and the patient sample. If base pairing happens between RNA in the patient sample brows, “I’ve had it up to here” with and the guide RNA, then Cas13’s wild reaction is triggered. Cutting the RNA probe discussions of germline editing. separates the fluorophore from the quencher so that if SARS-CoV-2 RNA is present in The technology has been applied to the sample, fluorescence occurs. many societal problems that are less In addition to adapting the chemistry from previous SHERLOCK applications, the fraught: agriculture, drug develop- team also came up with a detection box smaller than a shoebox with a stripped-down ment and nonheritable gene therapy, fluorescence excitation setup, which can be imaged using an ordinary cell phone to name a few. Most of the scientists running a custom app. Twenty-eight scientists, including biochemists, virologists, interviewed for this story mentioned biomedical engineers and physicists, were involved. Victoria Gray, an American whose sickle cell anemia was cured by edits FOZOUNI ET AL. MEDRXIV 2020 to stem cells extracted from and then transplanted back into her bone mar- row. CRISPR also has been used in basic research to understand topics as esoteric as the gene controlling snail shell spiral chirality. Meanwhile, the work to understand bacterial immu- lished cryo-EM structures of CasX, nity goes on — and the applications which unlike Cas9 makes a staggered for bacterial immunity effectors are cut in the DNA, producing sticky far from limited to Cas9. ends. Other bacterial effector proteins “Now we don’t have just plain va- cut RNA instead of DNA, produce nilla CRISPR–Cas9 that does DNA cyclic second messenger molecules or cutting,” Jinek said. “We have base simply bind specific sequences. With editors, we have prime editors, we input from engineers, the list of ap- have transcriptional control through plications for these protein functions CRISPR … all these applications that continues to grow (see “The many (are) still rooted in the basic molecu- uses for CRISPR” on page 38). JILLIAN BANFIELD lar principle of having a guide RNA Researchers have scrambled to find targeting double stranded DNA, but and lay claim to other effector pro- then apply all sorts of other molecular teins of bacterial immunity by scan- activities.” ning and mining bacterial genomes. Six general types of CRISPR Jillian Banfield, the Berkeley micro- system are known, and researchers use biologist who introduced Doudna them for different applications. Last to CRISPR in the first place, runs a year, for example, Doudna’s lab pub- company called Metagenomi mining
DECEMBER 2020 ASBMB TODAY 39 FEATURE
microbial genomes for novel gene- When asked what it was like to editing systems; the pharmaceutical have been instrumental to such an company Bayer recently invested $65 important discovery, Chylinski an- million in the enterprise. swered with a puckish grin, “It’s nice.” After a thoughtful pause, he added The future for CRISPR more seriously, “At the beginning scientists it was almost intimidating how fast things were going. … In some places What could I possibly tell you in the world, people are already get- about CRISPR technology that you ting experimental treatments partially haven’t heard before? There have based on something I did with my Joan Steitz knew Jennifer Doudna as a been about 48,000 research articles’ postdoc and a junior faculty member at Ph.D. thesis.” worth of new findings this year alone. Yale. “She didn’t need much mentoring, Both Doudna and Charpentier The technique has spurred close to a but everybody can stand some advocacy,” have worked on a variety of topics Steitz said. decade of explosive creativity in the over their careers, and as the CRISPR fields of biotechnology, basic biologi- field expands, they’ve found new areas cal research and clinical medicine, and within it to work on. it shows no signs of slowing. Charpentier has had a peripatetic “It often feels like the genome career, working in France, the U.S., engineering applications made pos- Austria, Sweden and now Germany. sible by CRISPR are limited only by “I could feel very quickly the right our collective imagination,” Doudna time to move on,” she told an inter- wrote in her memoir, “A Crack in viewer from The CRISPR Journal in Creation.” She used to keep a run- 2019. She said she wanted “not to ning list of organisms in which the get stuck in a position where maybe I technology had been used; that’s no would not evolve the way I wanted to longer possible. evolve.” Steitz observed that Doudna is Yogurt research, broad applications “interested in all sorts of very specific experimental problems and ques- After short repeating sequences interspersed with hundreds of diverse spacers were tions within the whole big realm of discovered in the 1990s, researchers found them in the genomes of more and more RNA and all its functions in cells. She bacterial species. CRISPR-associated, or Cas, genes, always seemed to travel with them. hasn’t been monolithic.” In 2005, CRISPR researcher Francisco Mojica raised the hypothesis that the spacers, Doudna agreed with that interpre- which matched phage sequences, could help bacteria recognize pathogens. The same tation and said her work is all about year, researchers reported that bacteria with more CRISPR spacers tended to be resistant a broader exploration of numerous to more phages. Then researchers at the yogurt company Danisco found that bacteria interesting problems. “When I think that acquired resistance to a phage also about how I choose topics, it’s more MARIUS WALTER/WIKIMEDIA picked up a spacer matching its genome. of a gut feeling,” she said. “It’s the The race was on to find out how bacteria things that I find interesting, or the absorb snippets of phage genome into things that I feel intrigued by, that their own — and how Cas family proteins tend to be the things I’m going to go use CRISPR RNA to find and destroy after.” phage DNA.
As it turns out, there are many Laurel Oldach (loldach@asbmb. answers. “It’s not like one mechanism org) is a science writer for the describes everything,” said Krzysztof Chylinski, who co-discovered the mechanism of one ASBMB. Follow her on Twitter @LaurelOld. Cas protein. “There are two classes, six types and, I don’t know, dozens of subtypes — and some uncharacterized systems.”
40 ASBMB TODAY DECEMBER 2020 Wednesdays | 12 p.m. EST Lipid Research Division Seminar Series
Weekly presentations from researchers highlighting their recent work in the field of lipids. Hosted by the ASBMB’s Lipid Research Division.
LEARN MORE AT: asbmb.org/meetings-events/lrd-seminar-series
ASBMB FELLOWS Call for nominations: the first class of ASBMB fellows
DEADLINE: JAN. 4, 2021
Selection as a fellow of the American Society for Biochemistry and Molecular Biology is an honor to be bestowed upon our most distinguished members.
The ASBMB Fellows Program encourages nominations that reflect the breadth and diversity of the society’s membership. Nominees must be regular, industry or emeritus members of the ASBMB.
asbmb.org/about/asbmb-fellows
DECEMBER 2020 ASBMB TODAY 41 HOLIDAY GIFTGUIDE 1 2
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DECEMBER 2020 ASBMB TODAY 43 FEATURE A global champion of ‘the big puzzle’ — biochemistry Alexandra Newton will be the third woman to serve as IUBMB president
By Arti Dumbrepatil fter more than three decades countries, promoting research and as a biochemist, Alexandra education throughout the world. The
COURTESY OF ALEXANDRA NEWTON ANewton remains on a quest to American Society for Biochemistry figure out how molecules interact and and Molecular Biology is a member of work with each other. Specifically, she the IUBMB, and Newton will be the wants to understand the mechanisms first woman ASBMB member to lead of target molecules such as enzymes the IUBMB. in maintaining human health and manifestation of disease. “For the development of effective Becoming a scientist therapies, in-depth understanding of As a little girl, Newton was the biochemical mechanisms is criti- intensely curious about science. “I cal,” she said. “Biochemistry is like a began experimenting very young,” she big puzzle, where you are finding and said. piecing together different pieces. A For her first experiment, instead new piece might take you into new of sending a baby molar to the tooth directions. It’s like I’m the detective fairy, she measured the tooth’s diam- working toward solving a problem, eter before and after submerging it considering all the clues available. in soft drinks to determine the sodas’ Alexandra Newton, president-elect of the IUBMB, There is never a dull moment.” effect on dental decay. “My parents displays her love of science in the form of her Now a professor of pharmacol- told me that soft drinks are not good favorite amino acid jewelry. ogy at the University of California, for you, but I wanted to find out San Diego, Newton has lived on myself,” she said. “So, I do not drink three continents and completed her soft drinks.” education in seven countries. Her During her undergraduate years at father was English, and her mother Simon Fraser University in Vancou- is from Cyprus. Born in Cape Town, ver, Canada, her teachers nurtured South Africa, she grew up in Canada, her interest in biochemistry. When Greece, France and other countries. she was a grad student at Stanford She speaks Greek, English, French and University, membrane biochemis- German. try sparked her interest. She did a These factors, along with her dedi- postdoc in Daniel Koshland Jr.’s lab at cation to biochemistry, helped New- the University of California, studying ton grow as a scientist and become a how lipids modulate the activity of mentor to students across the globe. protein kinase C, or PKC, an enzyme Now they will serve her as the third involved in metabolic regulation, woman president of the International immune signaling and cell prolifera- Union of Biochemistry and Molecular tion. Her work has helped research- Biology. The union unites biochem- ers understand the mechanism and ists and molecular biologists in 79 regulation of PKC.
44 ASBMB TODAY DECEMBER 2020 FEATURE COURTESY OF ALEXANDRA NEWTON
As a distinguished professor of found that PKC’s activity is enhanced Pictured at a 2019 conference in Kuala Lumpur pharmacology at UC San Diego and in neurodegenerative diseases: In are IUBMB Executive Committee members, left to co-director of the molecular phar- Alzheimer’s, a few atoms’ difference right, Past-President Joan Guinovart, who is from macology track in the biomedical in one isozyme of PKC increases its Spain; Alexandra Newton; Treasurer Francesco Bonomi, from Italy; and Chair of Meetings Ilona sciences graduate program, Newton activity, which, in a mouse model, is Concha Grabinger, from Chile. is an advocate for basic biochemistry enough to cause cognitive decline. research. She is also director of Cell Signaling San Diego, a new center An international vision that brings together local experts in the field. She continues to explore the Newton has been IUBMB’s pres- molecular mechanisms of cell signal- ident-elect since July 2018; she will ing and their deregulation in dis- become president in July 2021, and eases, with emphasis on her favorite past president in 2024 — a nine-year molecule, PKC, and the phosphatase commitment. Her vision as president PHLPP. is to foster scientific alliances that Newton’s team reversed a 30-year are inclusive about geographical and paradigm when they reported their gender diversity. The union already finding that PKC suppresses, rather provides opportunities to scientists than promotes, tumors. For decades, and students from developing coun- attempts to develop drugs that inhibit tries in programs such as Promoting PKC as a part of cancer treatment had Research Opportunities for Latin failed, she said. “Our study showed American Biochemists, or PROLAB, that we needed to develop anti-cancer a joint initiative with the ASBMB drugs that would boost PKC activity.” and the Pan-American Society for Newton uses PKC as an example Biochemistry and Molecular Biology of the importance of understanding that brings Latin American scientists the biochemistry of a target before to work in North American labs. developing therapies. Her lab has The IUBMB executive commit-
DECEMBER 2020 ASBMB TODAY 45 FEATURE COURTESY OF ALEXANDRA NEWTON tee has an equal number of men the time for scientists worldwide to and women, and Newton views the come together. She supports com- organization as a model for gender municating science across boundaries diversity. “It is tricky for our virtual in the form of virtual conferences and executive committee meetings at webinars, seeing the new necessity as the moment, which span 18 time an opportunity: “This pandemic has zones,” she said, “but our leadership also allowed me to open my courses team has members from all over the and lectures for students from differ- world.” ent countries.” Representation of women in She noted that the IUBMB now science has improved since Newton offers virtual conference fellowships, started as a graduate student; her allowing students from all over the Stanford class in chemistry included world to attend meetings. Alexandra Newton in her lab at UC San Diego with two women. Later, she was the only Newton is unfazed at holding a graduate student Alex Jones and postdoc Gema woman among 43 faculty members world leadership role. Lordén. in the Indiana University chemis- “I see a silver lining for the unusual try department. She is proud that year of 2020,” she said. “This pan- her department at UC San Diego demic has brought together scientists has equal numbers of men and around the globe. Physical boundaries women researchers, but she realizes did not stop scientists from trying to the difficulties women still face in work together. Virtual conferences the sciences, and she works to find have not only helped provide access to solutions that will promote inclusion a larger community but also bought and diversity in the field. out the innovative ways to communi- “I always tell anyone who is start- cate science.” ing a career in science, focus on the positives,” she said. “Follow your Arti Dumbrepatil (artidumbre@ gmail.com) is a science writer passion and love what you are doing covering topics ranging from The Newton Lab at their 30-year lab reunion with to overcome all the negatives.” nanorobots to virology. She has a Alexandra Newton at the bottom of the stairs and Other challenges have been Ph.D. in biochemistry and writes for Microbiome Digest and Bio the grad students in chronological order, with the subsumed by the COVID-19 pan- Voice News. Follow her on Twitter current ones at top of the stairs. demic, but Newton believes now is @rtisciwrites. TIM BAFFI
46 ASBMB TODAY DECEMBER 2020 PERSPECTIVES The Death Project by Robert J. Lefkowitz with Randy Hall
This piece is excerpted from “A Funny Thing Happened on the Way to Stockholm: The Adrenaline-Fueled Adventures of an Accidental Scientist” by Robert Lefkowitz with Randy Hall (published by Pegasus Books) due to be released Feb. 2, 2021.
he phone rang in my office, and when I answered it I received shocking news: my collaborator, the leg- Tendary Harvard structural biologist Don Wiley, was missing. Don and I had been collaborating on trying to determine the three-dimensional structure of the beta-2 adrenergic receptor. In the 1970s, my lab had pioneered the purification of the receptor, and in the 1980s we had discovered the receptor’s gene sequence. Now, in the early who knew Don, I became aware of all the details of 2000s, we were collaborating with Wiley’s group to per- the case. Don had been at a meeting in Memphis at St. form X-ray crystallography on purified beta-2 receptors Jude Children’s Research Hospital, where he served on a in order to see the receptor’s structure and understand research advisory board. He’d had dinner with some col- precisely how molecules like adrenaline bound to it. My leagues, and everyone at his table said Don was his usual lab was adept at purifying receptors and Don Wiley was upbeat and jovial self. Don left the dinner in a rental car one of the best X-ray to visit his father, who lived in the area, but then never crystallographers in the showed up at his father’s house. Police found Don’s car world, so I felt confident parked on the Hernando de Soto Bridge, a huge overpass about our chances for suc spanning the Mississippi River. One obvious possibil- cess. There was only one ity was that Don might have stopped on the bridge and problem: Wiley had now jumped to his death. However, Don had never shown vanished without a trace. the slightest hint of depression and by all accounts was in Don was an amazing especially good spirits that evening. scientist and brilliant wit who lit up every room he Conspiracy theories entered. He could give a talk about a seemingly dry As weeks passed without any break in the case, con- topic, like the structure spiracy theories began to pop up. Don was one of the Harvard structural biologist Don of a protein, and weave a world’s top experts on the structure of dangerous viruses, Wiley was “one of the best X-ray spellbinding narrative that such as the Ebola virus, which led some people to specu- crystallographers in the world” and would have an audience late that he may have been kidnapped by terrorists who an expert on infectious diseases, hanging on his every wanted to develop a biological weapon. This was shortly such as Ebola. word. As a storyteller after the terrorist events of 9/11, so terrorism was very myself, I recognized Don much on everyone’s mind. Others speculated that maybe as a kindred spirit and was thrilled to have him as a col- Don knew too much about some sort of dark secret and laborator. My affection and admiration for Don made his was murdered. Several other virus experts had died under unexplained absence all the more difficult to accept. mysterious circumstances around the same time, which Wiley’s disappearance became a national news story, only fueled speculation about Don’s case. so between reading the news and talking with colleagues About a month after Don’s disappearance, his body
DECEMBER 2020 ASBMB TODAY 47 PERSPECTIVES TREVOR BIRCHETT was leading the project, Serge Pares, died tragically (along with his pregnant wife) aboard TWA Flight 800, which exploded and crashed into the Atlantic Ocean shortly after takeoff in 1996. The project continued in the Sigler lab with contributions from several other postdocs. Then, in early 2000, Paul Sigler was walking near the Yale campus one day when he suddenly had a massive heart attack and dropped dead. Paul was a wonderful man and a hell of a scientist, so it was a devastating loss for all who knew him. One of the postdocs in Paul’s lab who was working on the project, Ben Spiller, then moved to the lab of Don Wiley at Harvard, and Don expressed an interest in continuing the collaboration with my lab. Thus, when Don’s body was pulled out of the Mississippi River on December 20, 2001, he was our third collaborator on this Don Wiley disappeared in November 2001 after a meeting in Memphis at project in six years to have met an untimely demise. In St. Jude Children’s Research Hospital. His car was found parked on the my lab, there was hushed talk about the X-ray crystal- Hernando De Soto Bridge, which spans the Mississippi River. lography studies being the “Death Project,” and concerns were raised that anybody working on this project might be cursed. was found in the Mississippi River about three hundred Though he had every reason to feel shaken, Ben Spiller miles south of Memphis. FBI agents and local law en- was undaunted by talk of a curse. After suffering through forcement officials examined his body and also performed the deaths of two consecutive mentors, Ben moved to the a careful examination of his car, which had some damage lab of yet another famous structural biologist, Stephen on the right front end. The official theory of Don’s death, Harrison at Harvard, and told me that he wanted to keep put forward by the Shelby County Medical Examiner, working on the project. Amazingly, Steve Harrison was was that his car had grazed a post on the bridge, which also on board with the idea. Steve had actually taken in led him to stop his car and get out to inspect the damage. quite a few of the mentorless young scientists from Don Somehow, he had then accidentally fallen off the bridge Wiley’s lab and was trying to help them continue their to his death. A large truck may have gone past, creating work. I called Steve and offered him the chance to decline a strong surge of wind that knocked Don off the bridge. this particular project, noting that the last two investiga- Alternatively, as Don did have an epileptic condition and tors who took on this collaboration were both now dead. was prone to the occasional seizure, he may have expe- In an act of defiance and bravery, Steve said he didn’t rienced a seizure event (perhaps related to the stress of believe in curses and was excited about the project, and hitting the post) and fallen over the railing. he insisted on continuing the collaboration with Spiller as In whatever way Don’s death actually happened, it the point man. was a jolt to the scientific community to lose a man who many thought might win a Nobel Prize in the next few Squirmy proteins years, and it was especially shocking to me, as we were actively collaborating with his lab. At the same time as these X-ray crystallography efforts were going on in my lab at Duke, we also had a number A cursed project? of other projects that were yielding interesting findings. For example, we were discovering novel G protein- One of the most macabre aspects of Don’s death was independent signaling pathways emanating from the that he was actually our third collaborator on the X-ray beta-2 receptor and other G protein-coupled receptors. crystallography project to die unexpectedly. Prior to While these groundbreaking studies were in full swing, collaborating with Don on this project, we had been we also were purifying large amounts of beta-2 adrenergic working with Paul Sigler at Yale. Shortly after that col- receptors on a weekly basis and sending these samples to laboration began, the talented postdoctoral fellow who Ben Spiller in Steve Harrison’s lab at Harvard. It was a
48 ASBMB TODAY DECEMBER 2020 PERSPECTIVES COURTESY OF ROBERT LEFKOWITZ
During a break from a scientific meeting in California in the late 1990’s, Bob Lefkowitz does his best to keep up with former trainees, Brian Kobilka and Sheila Collins, who by that time were both faculty members directing their own labs.
tough situation for Ben, having lost two mentors in tragic time to catch up with each other. Brian had been on the fashion and now doggedly trying to carry on his attempts Stanford faculty for about sixteen years at that point. to solve the crystal structure of the beta-2 receptor. At a dinner together during our visit in Illinois, Brian Technically, the project was incredibly demanding, confided to me that he had been focusing much of his as by definition receptors are squirmy proteins that are lab’s efforts on solving a crystal structure for the beta-2 prone to rapidly changing conformations. If you think adrenergic receptor. I told him that we also had pursued about it, that’s what receptors do for a living: rapidly efforts in this area for a while but dropped the project change conformations in response to ligands. Thus, it’s several years earlier because of concerns that success incredibly challenging to get a receptor to hold still for might not be possible with the current state of the tech- a photograph, which is basically what you have to do in nology. Brian said he also had encountered many techni- order to capture an X-ray crystal structure. cal difficulties and was simply hoping to get a crystal After a couple years of work on the project, Ben finally structure before he retired, perhaps at some point in the threw in the towel, and my lab moved on completely next twenty years. from the X-ray crystallography efforts because we were so When Brian said this, I patted myself on the back for focused on other interesting lines of research. Thus, when having the wisdom to drop the X-ray crystallography it came to the X-ray crystallography studies, aka the project and focus on other research directions, because it “Death Project,” the bad news was that we were unable seemed crazy to labor for twenty years trying to achieve a to solve the crystal structure of the beta-2 receptor. The goal that might end up being just a pipe dream. good news, though, was that no further deaths were as- sociated with the project: Spiller, Harrison, and the folks A dazzling leap in my lab who were pursuing these studies all survived to tell the tale. About a year later, in the spring of 2007, I received a A couple of years later, in 2006, my former trainee call from Brian with some surprising news. He said that Brian Kobilka and I shared a visiting lectureship at the his lab had achieved a number of technical breakthroughs University of Illinois at Urbana–Champaign. This joint and now had a crystal structure for the beta-2 adrenergic lectureship provided Brian and me with some quality receptor! Indeed, that November, Brian, Ray Stevens
DECEMBER 2020 ASBMB TODAY 49 PERSPECTIVES
and their collaborators published back-to-back papers several other labs, including the labs of Roger Sunahara, in Science describing the crystal structure of the beta-2 which had provided the purified G proteins used to achieve adrenergic receptor. These papers were a technical tour de the docked structure, and Yiorgo Skiniotis, which had force. Brian’s lab innovated at every step of the process: performed crucial electron microscopy work. This work improving the purification process to obtain much larger was even more of a tour de force than the 2007 papers quantities of pure receptor than was previously possible, reporting the first structure of the beta-2 receptor. If you engineering the receptor to be much more stable than think it’s hard getting one squirmy protein to sit still for a it normally was, and a dozen other technical twists that photograph, try getting two hyperkinetic proteins to hold other scientists couldn’t even dream up, much less actu- still and pose together long enough to take a perfect photo. ally attempt. The technical advances in Brian’s 2011 paper were stagger- This breakthrough had an enormous impact on the ing, and the structure was absolutely beautiful. Many new field, as everyone now saw the path forward to solving insights into how receptors work could be gleaned from the crystal structures for the hundreds of other G pro- this structure, and Brian went on a barnstorming tour to tein–coupled receptors encoded in the human genome. I describe his lab’s latest findings. was dazzled by this quantum leap in technical capability and absolutely thrilled for Brian, who had gambled a Nobel calling? great deal in pursuing these structural studies and now saw his gamble pay off in the biggest way imaginable. That summer, I was speaking at a Nobel Symposium What I didn’t know at the time, however, was that an in Stockholm. Brian was not giving a talk at the meeting, even more dramatic advance was on the way. but people were talking about him. He had just shown Several years later, in July 2011, Brian’s group pub- his receptor-G protein structure at a European biophysics lished a lead article in Nature reporting the crystal struc- meeting, and Gunnar von Heijne, a member of the Nobel ture of the beta-2 adrenergic receptor in complex with Committee for Chemistry, had witnessed the presentation. a G protein. This work was done collaboratively with He then returned to Stockholm for the Nobel Symposium COURTESY OF ROBERT LEFKOWITZ
In the lab, Bob Lefkowitz sketches out a plan of action with medical student Erin Bressler.
50 ASBMB TODAY DECEMBER 2020 PERSPECTIVES COURTESY OF ROGER SUNAHARA
Brian Kobilka and Bob Lefkowitz shared the 2012 Nobel Prize in Chemistry. This photo was taken just a few moments after the two finished their Nobel lectures.
where I was speaking, and when I chatted with him else in the world makes headlines for NOT winning the during a break in the meeting I could tell that he was Nobel Prize? In 2003, that headline had bothered me over the moon about Brian’s latest breakthrough. The a little bit. By 2011, I was just enjoying my day-to-day sentiment seemed to be shared by several other members work as a scientist and mentor, and was absolutely done of the Nobel Chemistry Committee who were attending with worrying about awards. Little did I know it then, the meeting. Of course, I had long ago given up try- but my life was about to change in dramatic fashion. ing to read into comments made by Nobel Committee members, as I had received many enthusiastic comments over the years from various Nobel Committee members Robert J. Lefkowitz ([email protected]) without ever being tapped for a Nobel Prize. is a Nobel Prize–winning scientist (Chemistry, 2012) That October, the Nobel Prize announcements came who is best known for showing how adrenaline works via stimulation of specific receptors. He was trained and went, and neither Brian nor I received a call from at Columbia, the National Institutes of Health and Stockholm. As usual, numerous people asked me ques- Harvard before joining the faculty at Duke University tions about whether I would ever win. I kept thinking and becoming an Investigator of the Howard Hughes Medical Institute. In addition to being a researcher, he about what Al Gilman said after he won his Nobel: “The is a cardiologist as well as a cardiac patient. best thing about winning the Nobel Prize is never again having to answer the question, ‘When are you going to win the Nobel Prize?’” Randy Hall ([email protected]) was a postdoctoral trainee of Robert Lefkowitz in the 1990s and is now a Admittedly, my situation in 2011 was not as bad as professor in the Emory University School of Medicine. it had been in 2003, when my local paper, the Durham He has published more than 100 scientific papers Herald-Sun, had run a front-page, above-the-fold photo- and received major awards for his research. He is also a prize-winning educator with strong interests in graph of me with a headline that read, “Nobel Calling? science writing and public outreach about science and Alas, Not This Year.” At the time, I was thinking: who medicine.
DECEMBER 2020 ASBMB TODAY 51 ESSAY Curbing the malpractice of curved grades and high-stakes exams By Melanie M. Cooper & Mike Klymkowsky
aculties on college campuses all over the U.S. Research also shows that grading on a curve with pre- responded to recent Black Lives Matter demonstra- determined outcomes has a disproportionate effect on Ftions with calls for a renewed commitment to a students in underrepresented and underserved minority more inclusive and equitable learning environment for groups. In a recent paper looking at outcomes in an in- our students. Many of us vowed to educate ourselves troductory general chemistry course at the University of about systemic racism through activities such as reading, Washington where grades are curved (around an average discussion groups and attending seminars. of a 2.6 grade points), researchers write that they found This work is necessary and important, but if you are a marked difference in the fates of students who received like us, you are ready for something more immediately a C in a course (and were able to continue) and those actionable that is under faculty purview and has been who got a C- and had to retake the course, despite the shown to produce more equitable outcomes. If so, we fact that there is little demonstrable difference in learn- suggest you look closely at your assessment and grading ing outcomes between the two groups. policies and think about their purpose. Faculty members Even more distressing are the different outcomes for have the opportunity to make immediate changes in these two groups of students. Underrepresented students these areas that can impact large numbers of students who were allowed to move to the next courses were and help to increase the diversity of the science, technol- more successful in terms of completing their degree ogy, engineering and mathematics student pool. programs than their majority peers. However, those who had almost identical grades but were deemed to have The curve failed (forced to repeat the course) were less successful than their majority peers. That is, a capricious decision It is well documented that some course policies to predetermine what percentage of the class must fail not only actively discourage students but are actively had a profound impact on underrepresented students. discriminatory. Two major research studies, “Talking What if these students had not been graded on a curve? about leaving” and its more recent updated companion What if 30% of the class had not been predetermined “Talking about leaving revisited,” both cite common ap- to fail? As David Asai noted in a commentary in the proaches to determining course grades as a major factor journal Cell, persons excluded because of their ethnicity for why students leave STEM disciplines. The practice or race, known as PEERs, “leave STEM at rates much of grading on a curve (that is, predetermining the higher than non-PEERs, and the pattern of poor PEER number of As, Bs and Cs that will be given in a course) persistence is essentially the same as it was nearly three sends the clear message that the purpose of the course is decades ago,” an outcome that may be due in part to to sort students and enforce competition rather than to grading practices. teach. While this practice seems intrinsically misguided to Rethinking assessments many of us, there is ample evidence that it survives — particularly (but not exclusively) in large introductory Certainly, some faculty might defend the practice of STEM courses. These courses typically are characterized curving as a way to prevent grade inflation, but this kind by what we call high DFW rates, meaning that a large of thinking is aligned with the sorting ethos — only the percentage of students are predetermined to receive a D, most deserving should be allowed through the gates into an F or a withdrawal grade that does not allow them to the promised land. Multisection large-enrollment classes continue on to the next course. often curve grades to ensure that grades are similar
52 ASBMB TODAY DECEMBER 2020 ESSAY
across sections, but wouldn’t it be fairer to set standards in such pathways. (mastery goals) and help students meet them? Rather than a few high-stakes tests, we could provide We need to rethink our approach to assessment, more lower-stakes checkpoints and other activities that moving from high-stakes tests that have almost no con- support desired learning outcomes. While some faculty nection to the actual things scientists do to an approach members inevitably will resist these suggestions (after that supports the development of knowledge in use and all, it is much easier to use publishers’ test banks that provides understandable goals for students. Our recent can be randomized and graded automatically), ample transition to remote education can provide us with the evidence exists that the curving practices discussed impetus to move away from the high-stakes testing that is here are exclusionary and inequitable. If we seriously so prevalent in many college classes and so detrimental to are committed to more equitable outcomes, we can many students. act to remove one known barrier for underrepresented Instead of obsessing about students cheating on students. high-stakes exams and going to extraordinary lengths to Now is the time to make these changes, before our prevent this by employing invasive technologies or ran- commitment to diversity, equity and inclusion fades domized multiple-choice exams that can test only recall and we go back to business as usual. Let’s seize the and rote exercises, now is the time to implement mastery moment and make some real changes that will directly learning, continuous assessment and alternate approaches benefit our students. to grading. What if we explicitly spell out what students need to know and what they must be able to do with that Melanie M. Cooper ([email protected]) is a professor of knowledge? Our learning objectives should lay out these chemistry at Michigan State University. requirements explicitly. Rather than requiring students to memorize and regurgitate the essential amino acids, what about ask- ing them to respond to prompts such as “Construct a representative amino acid structure and explain why these substances are soluble in water at pH 7” or “How do Mike Klymkowsky (michael.klymkowsky@colorado. differences between amino acids influence the folding of edu) is a professor of molecular, cellular and develop- mental biology at the University of Colorado Boulder. proteins or their catalytic activities?” Instead of having students memorize biological pathways, we could ask them to explain the role of adenosine triphosphate (or thermodynamically favorable and unfavorable reactions)
DECEMBER 2020 ASBMB TODAY 53 MINORITY AFFAIRS A history-making administration — ‘that believes in science’
A statement from the American Society for Biochemistry and Molecular Biology’s Minority Affairs Committee:
e congratulate President-elect Biden and Vice President-elect Harris on their election to the highest offices in the country. W Their election is a win not only for the United States, because we will have an administration that believes in science, trusts the data and respects researchers, but also for the world, because Biden and Harris have vowed to rebuild America’s relationships with allies and work with them to solve global problems, starting with the COVID-19 pandemic. In the U.S., more than 13 million people have been infected with the virus SARS-CoV-2, and more than 265,000 families have lost loved ones to the dev- astating disease it causes. Black, Latino and Indigenous communities have been affected disproportionately. The numbers are predicted to climb in the coming months, in part due to poor decision making at the highest levels of govern- ment. Already, though, Biden and Harris have already assembled a task force of experts to inform their COVID-19 plan, and they have promised to make decisions based upon evidence rather than politics. In 2020 alone, more than 160 Black lives have been taken by police. Our committee wrote about this issue in June, after the killings of George Floyd, Atatiana Jefferson, Breonna Taylor and others. We vowed to channel our grief and anger in productive ways. The election results tell us that millions of Americans did so at the ballot box. We are deeply relieved that Black lives mat- ter to the new administration, and we will continue to work to dismantle white supremacy and the systems that uphold it, including those in the academy. Immigrants, many of whom have worked hard to contribute to American society, and indeed American science, have been banned, scapegoated and tar- geted by the current administration. We look forward to having leaders whose immigration policies demonstrate both compassion for humanity and apprecia- tion for the contributions that immigrants make to the United States. We look forward to the new administration giving Dreamers the chance they deserve and ending the cruel and abusive policy of separating children from their parents at the border. The contributions of nonimmigrant foreign students and researchers to the American scientific enterprise cannot be overstated. The ASBMB policy team has done an excellent job of tracking and responding to the current administra- tion’s attempts to limit certain visas and discourage international collaboration. We have confidence that the new administration will maintain the United States’ standing as the world leader in science, technology, engineering and mathematics and as a beacon for the most talented and brightest minds.
54 ASBMB TODAY DECEMBER 2020 MINORITY AFFAIRS LAWRENCE JACKSON/BIDEN FOR PRESIDENT
Joe Biden announced U.S. Sen. Kamala Harris, D-Calif., would be his running mate on Aug. 12 in Wilmington, Delaware.
We are eager for the new administration to appoint an education secretary with expertise in education and to make decisions about STEM education based on best practices and evidence. It is also important to resume diversity, equity and inclusion training at the federal level and at federally supported col- leges, universities and institutions. Finally, the election of Harris to the office of vice president is especially mo- mentous and meaningful. She is a Black woman of South Asian descent — the daughter of immigrants — with a blended family. Harris’ election is evidence that not only women of color but women in general are brilliant, effective and well-qualified leaders. A woman in one of the two highest leadership positions in our country is empowering and long overdue. The members of the MAC enthusiastically look forward to a presidency during which decisions are made with consideration for scientific principles and knowledge, Black lives matter, and people are not discriminated against because of their ethnicity, race, gender identity or sexuality. As people who believe deeply in science and in the integrity of the scientific community, we recommend, as this new administration moves forward, that the policies and procedures put in place by the previous administration to politicize science, scientists and research be reversed so that our scientific community can move forward once again uninhibited to develop, design, innovate and report scientific findings in an unbiased manner and without fear of retribution. — Sonia C. Flores, Chair, ASBMB Minority Affairs Committee, with MAC members Ruma Banerjee, Kayunta Johnson–Winters, Deborah Neely–Fisher, Carlos Castañeda, Adela Cota–Gomez, Carlos Lopez, Vahe Bandarian, Gustavo Silva, Joseph Chaney, and Lana Saleh
DECEMBER 2020 ASBMB TODAY 55 Q QF “ You’ve got...to get outside of your comfort zone”
By Laurel Oldach can’t do anything without working with colleagues who have different ayne Fairbrother leads a expertise to put the pieces together department at Genentech and solve a problem. You’ve got to Wtasked with validating disease- be prepared to get outside of your associated targets and determining comfort zone. whether they are feasible for drug development. The biophysicist, who H ow has Genentech was raised in New Zealand and has changed in your time lived in California for decades, sat there? down virtually with ASBMB Today to talk about his career. The interview 3The company has gotten bigger. has been edited. In the early days we’d interact with everyone; now we’re spread over a larger campus, and it’s harder to know H ow did you come to work what’s going on everywhere at all Wayne Fairbrother at Genentech? times. You need to be more proactive in keeping your finger on the pulse. CURRENT POSITION 1It’s an interesting story. Genen- Also, the pendulum has swung a little tech was looking to set up a protein from basic discovery to more transla- Director and senior staff scientist, nuclear magnetic resonance group tional research. We’re all about mak- Early Discovery Biochemistry, back in the early 1990s. I applied for ing therapeutics for unmet medical Genentech the position and, as many people do, needs, so translation is critical. DEGREE got a polite “thank you, but no thank D.Phil., Oxford University, 1989 you” letter. Two or three months later I s there a project you’re I got a call from the director of pro- POSTDOCTORAL RESEARCH tein engineering, who had gotten my especially proud to have Scripps Research Institute worked on? name from one of their consultants, a FIRST JOB OUTSIDE OF ACADEMIA senior person in protein NMR who I There’s a clear winner there: a col- Scientist, Genentech knew — and I got the job. 4 laboration with Abbot Labs (now FAVORITE MOLECULE OR PROTEIN I like to tell that story to people AbbVie) and the Walter and Eliza looking for positions. You can get lost Hall Institute in Australia that Bcl-2 in the bureaucracy, especially nowa- resulted in a treatment for chronic days when everything is computer lymphocytic leukemia and acute evolving. When a target is considered searched, so having a network defi- myeloid leukemia. It’s a molecule that undruggable, it just means that we nitely helps. specifically targets Bcl-2, which for a haven’t discovered the way to drug it long time was considered undrugga- yet. That’s the way I like to think. A ny other advice ble. It was an exciting project — and you often give? it’s always fun to meet patients who Would you like to suggest an ASBMB have benefited from something that member who works in industry for 2I tell people going into industry you’ve touched. It reminds us why we a Five Questions interview? Send an the one thing I can guarantee is do what we do. email to [email protected]. that in five years they’ll be working on something completely different. I s there such a thing as Laurel Oldach (loldach@asbmb. org) is a science writer for the Things progress and come in and out an undruggable target? of favor for various reasons, whether ASBMB. Follow her on Twitter @LaurelOld. it’s science, strategic decisions or com- 5I don’t think there is. It may be petition. So you need to be flexible. true to say it’s not druggable with the That, and collaboration. You technology now, but technology is
56 ASBMB TODAY DECEMBER 2020 classifieds
Scientist, In Vivo Metabolism (Mass Spec) (AAV) Research Associate Calico Life Sciences Gene Therapy Vector Core Affinia Therapeutics
Calico is inviting applications from biologists Affinia Therapeutics is rapidly growing who are excited to be part of a scientific team biotech company developing transfor- dedicated to unravelling the fundamentals of the mative gene therapies for devastating aging process with a view to identifying targets diseases. We are backed by a strong and pathways suitable for therapeutic intervention. In particular, we are syndicate of life science investors and have ambitious plans to have a dramatic impact on the lives of patients around the world. looking for a scientist with a background in and deep knowledge of cellular and in vivo metabolism, who is interested in applying this train- As an early employee you will play a key role in setting our culture ing to advance our understanding of the role of metabolism in aging and values. You will be working alongside the founding manage- as well as the metabolic inputs and outputs to a variety of diseases ment team who have a track record of success in the industry. The pace of work will be dynamic, fast and fun. and signaling pathways. The successful candidate will be responsible for building and implementing new techniques to study the physiology We are looking for a curious, organized and self-motivated individual of disease and aging using cell culture, in vivo systems, stable isotope to work with our Gene Therapy Vector Core team. This is not a tracing, and mass spectrometry. typical Vector Core: our Vector Core is an integral part of our novel AAV discovery platform, and members work together to straddle careers.asbmb.org/job/scientst-in-vivo-metabolism-mass- spec/55230100/ the lines between research, process development, and support. This is an excellent opportunity to gain experience and develop in a dynamic, next-generation gene therapy environment. careers.asbmb.org/job/aav-research-associate-gene-therapy- vector-core/54958406/
AssistantHoward Hughes Professor Medical of Molecular Institute SeniorApplied Research BioMath, Associate, LLC Analytical BiophysicsPostdoctoral Associate & Biochemistry- Lefkowitz Lab DevelopmentSenior Scientist, Mathematical Modeler Yale University Allena Pharmaceuticals
The Department of Molecular Allena Pharmaceuticals, Inc. is a late-stage Biophysics & Biochemistry at Yale clinical biopharmaceutical company dedi- University invites applications for cated to developing and commercializing tenure-track Assistant Professor positions. We seek new colleagues first-in-class, oral enzyme therapeutics who will direct vibrant research programs in any area of molecular bio- to treat patients with rare and severe metabolic and kidney disorders. Allena’s lead product candidate, reloxaliase, is a first-in-class, oral sciences and who have an established interest in promoting equity and enzyme therapeutic for the treatment of hyperoxaluria, a metabolic inclusion among diverse scientists at any level. We welcome applicants disorder characterized by markedly elevated urinary oxalate levels and who use any approach to advance understanding of the molecular commonly associated with kidney stones, chronic kidney disease and basis of life. other serious kidney disorders. Its second product candidate, ALLN- Successful candidates will be expected to contribute to the excel- 346, is also a first-in-class, oral enzyme for the treatment of hyperuri- lence of a lively science community at many levels: they will direct and cemia and gout in the setting of advanced chronic kidney disease. support a research group in which diverse people can thrive, teach The Analytical Development Senior Research Associate will be respon- undergraduate and graduate students from diverse backgrounds, and sible for performing bioanalytical assays to support activities such be an interactive member of the department and the Yale community. as stability, characterization, and process development. Successful candidates should have laboratory training, experience working with careers.asbmb.org/job/assistant-professor-of-molecular-biophysics- biochemistry/55217995/ proteins and large molecules, experience maintaining laboratory note- books and providing data summaries. careers.asbmb.org/job/senior-research-associate-analytical-devel- opment/55230042/
To see a full list of jobs, please visit careers.asbmb.org The 2021 ASBMB Annual Meeting will be virtual!
LearnJoin us more April at 27–30,asbmb.org/annual-meeting 2021 Learn more at asbmb.org/annual-meeting ABSTRACT DEADLINE: Jan. 7
The ASBMB annual meeting is held in conjunction with Experimental Biology.