Department of
MICROBIOLOGY & MOLECULAR GENETICS NEWSLETTER FOR ALUMNI AND FRIENDS
SUMMER 2010
From the Department Chair...
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his year has been an important year for selfreflection as the department continues to deal with ongoing budget cuts. We have had to look at all programs with an eye to focusing on our strengths and have relied on our strength as a hub for both research and education. We have taken full advantage of our connections across the university and around the world. The university’s research expenditures from federal grants over the last 10 years have increased 58%, to $400 million this year, while state support has dwindled to only 32% of the total MSU budget. This illustrates the fact that research grants and philanthropy are rapidly replacing state funding for support of academic and research programs. The department is working hard at aligning these resources in a way that provides the best opportunities for students while at the same time focusing on scientific solutions that will benefit society. Building off our strong track record in microbial ecology, investigators in the department have worked in a symbiotic manner to integrate research in infectious diseases, genetics, the microbiome and evolutionary biology. We continue to leverage our strengths to provide growth and continue excellence in these areas. As evidence, we have had several recent significant accomplishments and expect more in the months ahead. Many microbiology faculty are involved in a recently funded National Science Foundation (NSF) Science and Technology Center (STC) built around evolutionary biology. This STC serves as one measure
Walter Esselman
of the strength of evolutionary biology at MSU. It also comes about 20 years after the NSF established the Center for Microbial Ecology – another major strength of our department.
Just recently we established the Enterics Research Center. The scope of this project is massive as it connects with many scientists across MSU. In addition to addressing one of the most important global health problems, diarrheal illnesses, this will provide increased opportunities for our students as they work alongside the many faculty involved in this project. We expect more opportunities in the months ahead as our faculty continue advancing research related to malaria, dengue fever, HIV, and water resource issues. The next few years will be a period of significant change for MSU as it refocuses on its core missions. Microbiology is well-positioned to play an important role in the future of MSU with our outstanding research and commitment to teaching. I hope you will read some of the articles in this newsletter and share my confidence in the future. Walt Esselman, Ph.D. Chair Department of Microbiology and Molecular Genetics Michigan State University
Chinese Academy of Sciences Recognizes Tiedje
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ames Tiedje was appointed to the Einstein Professorship of Chinese Academy of Sciences in the Institute of Urban Environment (IUE), Beijing, China. During the May 7, 2010 ceremony, Tiedje was awarded the professorship and delivered the speech “Biology’s Greatest Frontier: Our Microbial Allies in a Sustainable World.” Tiedje, considered one of the pioneers in modern microbial ecology, spent one week at IUE working with researchers. Tiedje has made outstanding contributions in the field of microbial dehalogenation mechanisms and respiration of halogenated organic compounds. He is director of the Center for Microbial Ecology and has published more than 350 papers.
Schmidt Receives ASM Teaching Award
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homas Schmidt was awarded the Graduate Microbiology Teaching Award for 2010 by the American Society for Microbiology. The award recognizes Schmidt for teaching, mentoring, encouraging subsequent achievement, and fostering an intellectually stimulating environment. Among MSU students, Schmidt is known for his ability to explain complicated material in a clear and concise manner while inspiring genuine interest among his students. He consistently encourages students to go beyond simple observation and to be quantitative in their research. Schmidt is a Fellow of the American Academy of Microbiology and his primary research interests are microbial community diversity and function.
WHEN A SPARTAN LOOKS TO CURE HIV
HE FINDS PROMISE IN NATURAL PROTEINS
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oughly five percent of people in the world are immune to HIV and dubbed ‘elite controllers.’ This term isn’t a statement about their personalities, rather it is commentary about how their cells control replication of the HIV virus. “When elite controllers are exposed to the HIV virus, they are just fine without any drugs or treatment,” said Assistant Professor Yong-Hui Zheng. “Our primary focus right now is to understand why these people are so resistant to the virus.” Zheng has spent ten years exploring this phenomenon and has discovered several proteins that have antiretroviral properties in humans. The family of proteins, called APOBEC3 proteins, prevent the HIV virus from replicating. The known proteins in the APOBEC3 family have led Zheng to suggest that humans have natural defenses that can stop HIV virus replication. However, the virus has evolved a viral infectivity factor (Vif) which prevents these proteins from working in patients.
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Zheng has been studying HIV resistance since his postdoctoral research at Vanderbilt University and the University of California, San Francisco. He came to Michigan State in 2005, and his research is funded by the National Institutes of Health. “Right now, my real thrust is to identify host genes with anti-HIV activity that the virus cannot take care of,” Zheng said. “Naturally occurring resistance is the best way for us to learn how to inhibit viral replication. No matter how smart human beings become, we can never beat nature. Nature has the best solutions and we must learn from these.” Identifying naturally resistant elite controllers can be difficult, as directly testing for resistance in humans is not an option. Instead, Zheng searches for resistance in human T-cell culture lines. “We successfully identified a T-cell line that was highly resistant,” Zheng said. “We saw a 100-fold or even a 1,000fold decrease in viral replication in the resistant cell line. We don’t know what it is yet, but it is very, very powerful since it restricts HIV replication so strongly.” Currently, Zheng along with his postdocs and students are testing the resistant cell line to determine what is preventing the HIV virus from replicating. Once they better understand what gives this cell line resistance, they will begin looking for this factor in the general population.
Yong-Hui Zheng
“Everybody in my lab is so excited,” Zheng said. “We’re trying to really identify this factor, to understand how it works, and ultimately develop a new treatment strategy once this factor has been identified. This is leading-edge science where we can have a great impact.”
Department of Microbiology and Molecular Genetics
IN THE CLASSROOM, SPARTANS WRITE, REVIEW AND PUBLISH.
THEY APPLY WHAT THEY HAVE LEARNED AND SHARE WITH THE WORLD
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he fifth edition of the Basic Biotechnology eJournal was released on the Internet in December 2009. Since its inception five years ago, more than 100,000 papers from the journal have been downloaded.
While this is a feat for an open access journal, the most impressive part is that all of the content – from writing articles to peer review – is accomplished by undergraduate students as part of the Microbial Biotechnology (MMG 445) course. In the course, students work closely with faculty and their classmates to produce content for the open-access journal and publish their articles as a part of their coursework. The student-produced articles have been downloaded by readersin more than 100 countries and some individual papers have been downloaded more than 5,000 times. “The journal showcases what MSU students are capable of,” said George Garrity, professor for the class. “The writing and editing process allows the students to use what they have learned throughout their MSU careers to synthesize questions, actively learn and clearly express their ideas about a wide range of topics.”
approach in 2004 because he felt it would make his students more successful employees or graduate students. “Critical reading, writing and thinking are among the most highly valued skills in the biotech industry, and this method forces them to apply their scientific skills,” Garrity said. The class combines lectures, open question periods and new technologies. Students attend weekly lectures, watch prerecorded lectures and comment on a class blog. The blog allows students and professors to interact constantly throughout the semester.
Open Access eJournal The MMG 445 e-Journal averages 2,000 unique visitors per week. Over the last six months, 14,000 visitors came from 123 countries. Among the most popular downloads is a 2007 publication by Brian Denton, Advances in Phytoremediation of Heavy Metals Using Plant Growth Promoting Bacteria and Fungi, which has been downloaded nearly 5,000 times. The journal is at: http://bit.ly/MMG445.
As a final project, each student writes a scientific paper that is then reviewed by a panel of their peers. Each student participates in four peer reviews in evaluating papers written by other classmates. Garrity adds that student involvement in both activities leads to a greater understanding of the whole process.
“Students learn to look for areas that need improvements, ways to improve clarity,” Garrity said. “We also put a strong emphasis on making sure the science is consistent.” The journal, articles and student presentations are available online at: http://bit.ly/MMG445.
The MSU Department of Microbiology and Molecular Genetics newsletter is published annually by the College of Natural Science for alumni and friends. Copyright 2010 Michigan State University. MSU is an affirmativeaction, equal-opportunity employer. Send correspondence to: Dept. of Microbiology, c/o CNS Advancement Office, 103 Natural Science Building, East Lansing, MI 48824. Ph (517) 353-9855. E-mail: natsci4u@msu.edu. Contributing writers: Walt Esselman, Gordon Shetler, and Mike Steger. Photography: Gordon Shetler, Mike Steger, G. L. Kohuth, istockphoto.com, MSU University Relations.
Garrity launched this applied
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Scientists Study Evolution in 50,000 Generations of E. Coli
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alking into Richard Lenski’s lab in the Biomedical and Physical Sciences Building provides a panoramic view of Spartan Stadium, the MSU Dairy Store and the Capital dome. The unassuming incubator humming away at the end of a lab bench and the dozen gyrating flasks yield no clues to their notoriety and importance. Richard Lenski, Hannah Professor of Microbial Ecology, started the E. coli long-term evolution experiment in 1988. The inexorable rhythm of the project continues daily as cultures are propagated, samples are frozen, and generations evolve. The experiment is essentially a time machine. Samples are frozen at each 500 generation stage, allowing Lenski and his students to retrace evolution as it occurs. And the E. coli have evolved. One major breakthrough came in 2003 after 33,000 generations. The E. coli evolved a new way to eat and began using citrate – a secondary resource that their ancestors could not use – as food. The frozen samples allowed Lenski and his students to replay the experiment
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and determine the role of earlier genetic changes in this breakthrough. The findings, published in 2008, quickly became a benchmark study in evolution as it documented evolution in action. In February, the 22nd anniversary of the experiment brought another milestone: 50,000 generations. Watching that same number of generations in humans would take around one million years. Studying evolution, however, goes beyond the lab. Just days after the 50,000 generation milestone, a team of MSU faculty, anchored by Lenski, was awarded a Science and Technology Center (STC) grant by the National Science Foundation. The $25 million grant unites biologists who study natural evolutionary processes with computer scientists and engineers who are harnessing these processes to solve realworld problems. The Bio/ computational Evolution in Action CONsortium, or BEACON, involves more than 30 faculty in four MSU colleges and four other universities. “We have an incredible opportunity now for the two-way flow of ideas and methods between biology and engineering,”
Department of Microbiology and Molecular Genetics
said Lenski. “We can use deep biological principles to stimulate innovation in computational realms and, at the same time, use the speed and precision of computers to explore open questions in biology.”
tify changes in organismal fitness, measured spontaneous mutation rates to discover changes in DNA-repair functions, and sequenced entire genomes to find all of the mutations responsible for the fitness gains and other phenotypic changes.
Students in the lab aim to integrate understanding of these genomic and phenotypic changes by identifying and manipulating both genetic and ecological variables. The long-term evolution experiment Richard Lenski pulls frozen bacteria cultures out is their time of a freezer in his lab. machine for continuing the The data and concepts study of evolution in acprovided by biological tion – a concept suggested scientists will enhance the by Charles Darwin and one development of computer playing out on the sixth models and engineered floor of the Biomedical and systems. The understandPhysical Sciences Building. ing of evolution will be applied to create new Lenski’s research is funded technologies and to solve by the NSF and other problems ranging from federal agencies, as well as the development of safer an endowment honoring cars to systems that detect long-time MSU president computer intrusions. John Hannah. Students in the Lenski Lab are With a cadre of underfunded through research graduate and graduate fellowships, undergraduate students, Lenski’s lab has research scholarships emerged as a leader in the and other endowments study of evolution. They established through have performed competiprivate support. tion experiments to quan-
Building Relationships to Improve Water Quality Spartan Leaders Work With Singapore to Model and Advance Understanding
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team of faculty leaders traveled to Singapore in January to develop relationships in the area of water science. The island city-state serves as a model for studying water and the systems it has in place. “We believe there is much to learn from Singapore, which has established itself as a world leader in water science and technology,” said Walt Esselman, department chair. “Singapore represents an opportunity to learn from the best, create international collaborations with world-recognized leaders in water, and learn from their experience and to become a partner with global water groups.” Esselman explained that MSU is uniquely positioned as a leader in water science, technology, education and entrepreneurship. In addition to the abundant natural resources in Michigan, the university is home to researchers who are already working hard to address future water demands from increasing population and climate change effects. At the MSU Center for Water Sciences, interdisciplinary teams of faculty and students study topics that include antibiotics in water and the development of microbial resistance, viral pathogens and waterborne disease, and the complexity of natural and human influences on biodiversity.
Joan Rose, the Homer Nowlin Endowed Chair of Water Research, has been involved in the investigation of waterborne outbreaks worldwide. Her work has examined new molecular methods for waterborne pathogens and zoonotic agents such the parasite Cryptosporidium and enteric (intestinal) viruses. Rose studies water supplies, water used for food production, coastal environments, drinking water treatment, wastewater treatment, reclaimed water and reuse. She is specifically interested in microbial pathogen transport in coastal systems and risks to recreation. Another faculty member in the Center for Water Sciences is R. Jan Stevenson, professor of zoology. Stevenson studies algal communities. He uses algal taxonomy and ecology to test ecological theory and to develop approaches for solving environmental problems. He is particularly interested in how ecological systems respond to environmental change. He also works with federal and state officials to develop protocols for ecological assessment.
Jay Lennon, professor of microbiology and molecular genetics, studies the effects of resource and environmental variability on ecosystem structure and function. His research efforts include questions related to the spread of invasive species, cultural eutrophication, microbial controls on carbon flow, and the influence of nutrient supply on the co-evolution of marine viruses and their bacterial hosts. “Building the relationships between MSU academic leaders and officials in Singapore provides a stronger network for our research,” Esselman said. “As water science becomes increasingly important world-wide, we will be able to rely on our global network to help develop solutions for fresh water, both in the Great Lakes region and in other communities around the world.” Several faculty from the department are participating in Singapore International Water Week 2010. For details on their involvement, go to http://bit.ly/msuwaterweek.
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New Method Provides
Understanding of TauD Enzyme’s Inner Workings
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Junior Named Goldwater Scholar
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asneem Pierce wants to understand how genes interact with each other – and she uses chickens to do it. That curiosity, coupled with her love of research, has earned the junior majoring in genomics and molecular genetics a spot as a 2010 Goldwater Scholar.
sing a new cooling method, a team of MSU scientists has uncovered the inner workings of bacterial enzyme, Taurine/ alpha-ketoglutarate dioxygenase, known as TauD.
Pierce is from Grand Rapids, Michigan, and is Michigan State’s 28th Goldwater Scholar. She is vice president of the Microbiology Club and also manages the research lab of C. Titus Brown, assistant professor of microbiology and molecular genetics.
Robert Hausinger, professor of microbiology and molecular genetics, led the team that was investigating how iron and oxygen atoms reacted together in TauD. The enzyme serves as a model for many other proteins, so increased understanding has implications in the scientific and medical fields in development of new medicines and how enzymes repair DNA.
“Tasneem’s experience in the lab, as well as the classroom, has provided her many opportunities for advanced study in gene regulation, evolution and understanding the mechanisms of development,” said R. James Kirkpatrick, dean of the College of Natural Science. “We are proud to have provided her a strong foundation for her success as a future leader in science.”
Since the reactions often are complex, fast and require multiple steps, the MSU team developed a new method to follow Robert Hausinger the TauD reaction. The difficult part was to slow the reaction down enough so that the individual steps could be observed. The team used a stream of cold nitrogen gas to slow down the reaction at -36 C. To prevent freezing and to keep the reaction going, they used
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Tasneem Pierce
“It is very exciting that Tasneem Pierce has been selected as a Goldwater Scholar; it is a well-deserved honor,” said Cynthia Jackson-Elmoore, dean of the Honors College, who is MSU’s official representative to the Goldwater Foundation. “Tasneem’s success is another example of what students accomplish through hard work, dedication, commitment and a strong mentoring relationship with faculty. The Goldwater Foundation plays an important role in helping MSU and other research universities assist students in following their research passions.” The Goldwater Foundation awarded 278 scholarships this year to mathematicians, scientists and engineers..
ethylene glycol - the same antifreeze that goes in vehicles. Once the reaction started, the team used lasers - in an advanced method called Raman spectroscopy - to follow the vibrations of iron and oxygen atoms in TauD to determine how the reaction progressed. They discovered never-seen-before steps in the TauD reaction, overturning conventional thought.
Department of Microbiology and Molecular Genetics
The project was a collaboration between Hausinger and Denis Proshlyakov in Department of Biochemistry and Molecular Biology, with support from colleagues at Argonne National Laboratory. The research, supported by the National Institutes of Health, was published in the Proceedings of National Academy of Science.
Richard Gilpin, Ph.D. ’70, is President and CEO of R. Gilpin, Limited, a biosafety consulting company that includes the GTS Legionella Water Testing Laboratory based in Gaithersburg, Maryland. He co-directs an internationally recognized biosafety course entitled Hopkins’ Control of Biohazards Course. Gilpin is a Registered Biological Safety Professional, a Certified Biological Safety Professional, a past Councilor (elected Officer), and past Chair of the Technical Resources Committee of the American Biological Safety Association (ABSA); a past president of the Chesapeake Area Biological Safety Association (ChABSA); and a 35-year member of the American Society for Microbiology. David Odelson, Ph.D. ’84, is Chief of Staff and Director of R&D Operations for a 450 member research staff in Genetic Systems (focused on nucleic acid sequencing and applied markets) in Life Technologies Corp. (formerly Invitrogen and Applied BioSystems). Michael Thompson, ’84, received a Meritorious Service Medal in 2009 for contributions to orthopaedic training at the Naval Medical Center San Diego. Thompson retired from active duty in the U.S. Navy in 2009 and is now with the Scripps Clinic
Medical Group in San Diego as codirector of the section of Hand and Microvascular Surgery within the Division of Orthopaedic Surgery. In addition to other decorations and awards, Thompson received a Bronze Star in 2007 for service in Iraq. Mark Terry, ’86, published his 4th novel, The Fallen, in April. This is his third novel featuring Homeland Security troubleshooter Dr. Derek Stillwater, an expert in biological and chemical terrorism, and is published by Oceanview Publishing. Booklist recently reviewed it, saying: “Tense from the first page, The Fallen maintains its intensity up to the very end, and Stillwater is both a sympathetic and believable hero. Readers of previous Stillwater novels will eagerly wait to see him in action again, and those new to the series will seek out his earlier adventures.” Dan Beacom, ’87, is the Principal Microbiologist, Fermentation Development Group Leader at Cargill Bio TDC. In March, Beacom presented the award lecture when Cargill received the 2010 ACS Industrial Biotechnology Award. His group at Cargill developed and commercialized a low pH lactic acid fermentation using a yeast host – a process which significantly reduces both the cost and environmental footprint of lactic acid production
resulting from the traditional neutral pH fermentation and acidification process. His particular role was in scaling-up the process from the lab through large scale trails and into production. Jason Pratt, M.S. ‘05, a yeast and fermentation scientist at MillerCoors, was featured in the the May 2010 issue of Black Enterprise magazine. Pratt appeared on the cover and was featured in the article “The Transformers - Tech-, science-, & math-savvy young professionals inject innovation and reset the system”. Travis Reed, ’05, D.V.M. ’09, is currently doing a small animal rotating internship at the Ontario Veterinary College at the University of Guelph in Guelph, Ontario. He will be moving to Rochester, New York, to begin a small animal surgical internship in July. David Stepien, ’07, M.S. ’08, is finishing his second year of medical school as part of a M.D.-Ph.D. program at Boston University School of Medicine. He is preparing to enter his first year of Ph.D. study in the Department of Pathology at BU. Send us your career news NatSci4u@msu.edu
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DEPARTMENT OF MICROBIOLOGY & MOLECULAR GENETICS College of Natural Science 103 Natural Science Building East Lansing, MI 48824-1115
We love to share alumni success stories with microbiology students. Stay connected Join microbiology alumni on Linked In and Facebook www.mmg.msu.edu
for details.
Annual Alumni Gathering at ASM Meeting The department hosted its annual alumni reception at the American Society for Microbiology conference in San Diego, California, on May 25, 2010. More than 100 people attending the reception enjoyed an evening talking with alumni, faculty and current graduate students. Among those attending were (top photo, left to right) Professor James Tiedje, Gerard Stelma (Ph.D. ‘74) and James Johnson (Ph.D. ‘71) as well as (bottom photo, left to right) Department Chair Walt Esselman, Nolin Chair of Water Research Joan Rose, and University Distinguished Professor James Tiedje.