Department of Microbiology & Molecular Genetics NEWSLETTER FOR ALUMNI AND FRIENDS
Recent Microbiology Initiatives and Highlights at MSU
reetings to all friends and alumni of the Department of Microbiology and Molecular Genetics. I am proud to have this opportunity to bring you up-to-date on some of the accomplishments and exciting programs we have happening everyday in the department. Walt Esselman I am pleased to report that the department has weathered the economic woes of the past couple of years in relatively good shape. This issue tends to be one of the first questions alumni often ask me, and you can rest assured that due to the careful planning of administrators who had the foresight to anticipate the direction the economy was going, we spread budget cuts over multiple years and were able to keep the academic mission of the university as protected as possible. Credit is also due, however, to the hard work of departmental faculty. Their ability to collaborate across the university and forge relationships has contributed significantly to several highly successful research initiatives. This illustrates the breadth of our research strengths as well as our overriding emphasis on integration among scientific disciplines. These initiatives build upon our strengths and continue to allow us to gain exposure among the scientific community. Yet most importantly, every one of these allows our students to become deeply involved in amazing new areas of science. It is easy to see how students benefit from having
a world-class researcher be their class instructor for a semester. What is even more amazing is the increased number of students, both undergraduate and graduate, who are now working alongside these faculty in their labs. Combining the handson learning with the unique research our faculty are conducting is providing the next generation of scientists with an unparalleled opportunity. Every alumnus should feel proud of not only the research we are doing to solve some of the toughest problems, but that we are involving students at every level of the work. This exposure and experience will undoubtably provide massive dividends in the years to come. Here are a few highlightss of programs our faculty are involved with:
Evolution in Action â€” One of the most exciting events in the past two years was the announcement that MSU was picked by NSF to establish a Science and Technology Center called BEACON (Bio-computational Evolution in Action CONsortium). The BEACON offices are in our building and numerous faculty in the department play key roles, including Richard Lenski who is one of the PIs. As for teaching, we continue to be proud of the diversity and quality of our undergraduate program. Last year we served 350 undergraduate students majoring in microbiology and genomics. However, that number tells only a small part of our teaching as we also served several thousand students majoring in Human Biology and other life science programs at MSU. We anticipate an even greater number this fall as the College of Natural Science experiences an even greater amoun amount of incoming freshmen going in into life sciences or indic indicating they are pre-med.
F Finally, I encourage yyou to stay in touch Water Science â€” Visit w Recognizing the with the department, mmg.msu.edu w success of the MSU whether you are a for the latest ccurrent student yet to Center for Water department news & fo Science, the university forge your own path in information the world or a long lost has decided that water or alum. P will be a signature area for Please feel free to write me directly investment in the comingg years. directly, or to get in touch via Several microbiology faculty have been the web site: mmg.msu.edu. instrumental in winning grant support to Walt Esselman, Ph.D. study both scientific and policy questions Chair, Department of Microbiology and regarding water in the Great Lakes region Molecular Genetics and beyond. Michigan State University
Recent Alumnus Stays to Study Speciation of E. coli
he ink is still fresh on Zack Blount’s diploma, but he already has big plans for the next stage of his career. Blount received his PhD from MSU this spring after finishing his dissertation on aspects of E. coli evolution under the guidance of Rich Lenski. Now Blount is beginning a research project to determine if a new species has evolved right here at MSU. “These experiments have been on the drawing board for years, and it is wonderful to finally get to them,” Blount says. His work is supported by a postdoctoral research position with the microbiology department and BEACON, the NSF-funded center for evolution studies. For Blount, staying at MSU was a natural choice. “MSU’s facilities for doing genomics and sequencing and a variety of other large-scale, complicated molecular work are fantastic,” he says. “The Research Technology Support Facility is unparalleled.” The facility provides technical and analytic support to MSU researchers and has helped the Lenski lab build a database of genomic information on clones taken from 12 populations of E. coli that Lenski has studied and evolved in the lab since 1988. Additionally, BEACON provides an advantage to conducting this research. Blount is able to meet regularly with other scientists who are studying speciation and the collaborators each provide additional strength to the program. Blount says they all offer insight and experience that other scientists can use, even though the subjects studied differ. “Even if there isn’t experimental collaboration, there is conceptual cross fertilization,” he says. In 2008, Blount and Lenski reported that a mutant had evolved in one of the long-term populations that could
bacteria to their new way of life. To find these, he will move mutations into an early Cit+ clone, and see if they give an evolutionary fitness benefit. Once Blount finds mutations that are beneficial to Cit+, he can move them into a Cit– strain that can’t grow on Zack Blount is using genome data to determine if a new species of E. coli has citrate, and see if they still confer a evolved in an MSU lab. fitness benefit. If the mutations are do something that E. coli should not – + , then they would be detrimental to Cit be able to do. This mutant, called Cit , a barrier to successful horizontal gene had learned to grow on a substance in + – transfer between Cit and Cit . Blount their growth medium called citrate. The says this inability to successfully transfer inability to grow on citrate is one of the genes would support the argument that traits that is used to define E. coli as a Cit+ is a new species. species. Blount’s new research will focus on the question of whether or not Cit+ is a new species.
Blount estimates that it will take at least 2 or 3 years to test whether or not Cit+ meets this definition of speciation.
“It is difficult to define speciation in bacteria like E. coli because the clearest sign that two groups of organisms are separate species is that they can’t reproduce together,” says Blount. “But bacteria reproduce asexually, so other definitions have to be used. Speciation is a tricky concept because you can’t use the same definition with all organisms.”
“Demonstration of speciation is the Holy Grail of the series of experiments that I have planned,” says Blount. “I can’t wait to see how these experiments unfold, and if the Grail really is there at the end of the quest.”
While they don’t have sex, bacteria do engage in horizontal gene transfer and can trade genes back and forth. Blount will use the inability to successfully trade genes back and forth as a test for whether or not Cit+ represents a case of speciation in the lab. He will use the genome information the Lenski lab has accumulated over the years to identify mutations that have accrued in the Cit+ population since it learned to grow on citrate. Some of these mutations will have adapted the Cit+
Department of Microbiology & Molecular Genetics
The Department of Microbiology & Molecular Genetics newsletter is published annually by the College of Natural Science for alumni and friends. Copyright 2011 Michigan State University. MSU is an affirmative-action, equal-opportunity employer. Send correspondence to: CNS Advancement 5 Natural Science Building East Lansing, MI 48824 Phone (517) 353-9855 E-mail: firstname.lastname@example.org Contributing writers: Walt Esselman, Angela Hobson, Michael Steger. Photography: Angela Hobson, Michael Steger, MSU University Relations.
Away From Petroleum: Using Bacteria to Produce Organic Acids From Organic Waste
laire Vieille is not afraid to chase her dreams. After receiving her PhD from the Institut Pasteur in France, she attended a lecture by MSU Professor J. Gregory Zeikus on his work studying enzymes produced by thermophilic bacteria. Vieille was hooked. She left Paris and headed for East Lansing. “Chicago or New York would not have been as much as a shock as Lansing,” Vieille says. Unphased, Vieille charged forward with her career. That was 18 years ago and her impact on MSU students and research continues to grow. Vieille, an assistant professor of microbiology, was recently awarded a $1 million grant from the USDA to study how to use the bacterium Actinobacillus succinogenes and the feedstock glycerol to produce succinate.
The grant supports a research project that has been 10 years in the making. Her research into succinate production is a form of bio-production. Succinate is used to make polyesters, solvents, nylons, and resins for the auto industry and is currently made from petroleum. Vieille’s system uses a naturally occurring bacterium, Actinobacillus succinogenes, which is fed glycerol and produces succinate. This bio-production system could help wean a portion of the chemical industry from a petroleum product. The system uses glycerol - a by-product of biodiesel production. “The idea is that we need to use cheap renewable feedstocks to produce these chemicals, and glycerol is an obvious one because it is a waste product of biodiesel production,” Vieille says. “It would help biodiesel production by making it more sustainable and it would help the chemical industry switch from a petroleumbased to a biomass-based feedstock.” As an added benefit of this system, the bacterium is a consumer of CO2.
Nick McPherson, a graduate student in the Genetics Program, and Claire Vieille in the lab where Vieille is researching ways to use bacteria to help replace petroleum in making succinate.
In 2009, Vieille received a grant from the Michigan Economic Development Corporation to help continue
her work. This funding was critical for the project as it allowed her research to reach a new level, she notes. The latest USDA grant helps extend the research and continue the discovery. Vieille’s research has opened interesting avenues for student participation and interdisciplinary research. Her interest in creating a microbial fuel cell which would produce succinate and electricity at the same time led to a cooperative effort with the department of chemical engineering. As part of a class, two chemical engineering students are assisting Vieille in constructing the cell. While a long way from the ChampsElysees, Vieille is at home at MSU as her research explores new avenues in molecular biology to help combat climate change and support the search for alternative fuels.
Malaria Research The National Institutes of Health has established a malaria research center at MSU - one of ten centers around the country. Ned Walker, professor of microbiology, is part of the research center led by Terrie Taylor, University Distinguished Professor in the College of Osteopathic Medicine. The $9.1M grant allows MSU to develop a self-sustaining research center capable of implementing and evaluating anti-malaria strategies and focuses on battling malaria Malawi. MSU researchers are using advanced molecular and genomic techniques to study the malaria parasites, the mosquitoes carrying the parasite, infected patients and people who carry the parasite but manifest no symptoms themselves. Malaria is estimated to kill as many as one million children each year in subSaharan Africa. Michigan State University 3
In Evolution, Adaptability Prevails Over Short-Term Fitness
esearch published earlier this year in the journal Science received international media coverage for Richard Lenski, Hannah Distinguished Professor of Microbiology and Molecular Genetics, and colleagues. The New York Times, Discover, Nature and media around the globe reported on the findings which showed that more adaptable bacteria oriented toward long-term improvement prevailed over competitors that held a short-term advantage.
“In games it makes sense to sacrifice some pieces for an eventual winning move,” said Lenski. “The eventual winners were able to overcome their short-term disadvantage over the course of several evolutionary moves by producing more beneficial mutations.” Lenski is recognized as a leading evolutionary experimentalist. He and his team revived a frozen population of E. coli and compared the fitness and ultimate fates of four clones representing two genetically distinct lineages. One lineage eventually took over the population
Ayers Receives Outstanding Alumni Award
he MSU College of Natural Science presented Eric Ayers (B.S. Microbiology ’85) the annual Outstanding Alumni Award for 2011. Ayers is the program director of the combined internal medicinepediatrics residency program at Wayne State University. Since 1994, Ayers has been an assistant professor in the departments of Internal Medicine and Pediatrics at Wayne State. He attended medical school at Wayne State and did his residency at Detroit Medical Center and also completed a threeyear fellowship in substance abuse sponsored by the National Institutes of Health.
Microbiology alumnus Eric Ayers received the Outstanding Alumni Award from Dean R. James Kirkpatrick during the CNS Awards Ceremony in April 2011.
even though it had significantly lower competitive fitness than the other lineage that later went extinct. By replaying evolution over and over with the clones, the researchers showed that the eventual winners likely prevailed because they had greater potential for further adaptation. “In essence, the eventual loser lineage seems to have made a mutational move that gave it a short-term fitness advantage but closed off certain routes for later improvement,” Lenski said. “And the dead-end strategy allowed the eventual winners to catch up and eventually surpass the eventual losers.” Lenski’s collaborators include co-author Robert Woods, an MSU alumnus who worked in Lenski’s laboratory and is now a physician scientist at the University of Michigan; Jeffrey Barrick, another Lenski lab researcher now on the faculty at the University of Texas; Tim Cooper from the University of Houston; MSU undergraduate student Mark Kauth; and University of Houston student Utpala Shrestha. While Darwin’s theory of natural selection has been confirmed by a great deal of other research, it has never before been observed directly for so many generations and in such detail as Lenski’s 25-year experiment has afforded. Lenski’s research is supported by the National Science Foundation, the Defense Advanced Research Projects Agency and MSU AgBioResearch.
Ayers’ commitment to medical education exceeds the boundaries of his faculty position. He serves as an alumni advisor for MSU’s Charles Drew Science Scholars Program - a program providing academic and social support for high achieving students pursuing science and math degrees. Ayers also mentors elementary, high school and college students in their pursuit of success. Ayers work and advocacy have earned him distinctions ranging from the Detroit City Council’s “Spirit of Detroit” Award to the peer-driven “Outstanding Doctor” Award. He has also received many accolades, including Outstanding Teacher by the WSU School of Medicine, the Pfizer Humanism in Medicine Award and the Leonard Tow Award for Humanism in Medicine.
Department of Microbiology & Molecular Genetics
Follow the BEACON Blog at beacon-center.org to see how students and scientists in biological evolution and computer science are changing the world.
Theoretical Physicist is at Home Among Microbiologists
hristoph Adami has a PhD in theoretical physics, yet he is the newest member of the faculty in the Department of Microbiology and Molecular Genetics.
While this non-traditional partnership may seem odd at first glance, it has potential to take evolutionary biology research into many new areas. Adami first came to MSU last year while on sabbatical from California and as part of BEACON - the National Science Foundation’s Science and Technology Center headquartered at MSU. The center studies evolution in action and involves many faculty from the microbiology department.
“Simulations are the theory of today,” Adami says. “You really cannot do theoretical biology using equations anymore as the systems are too complex. Simulations are an extension of equations and they go where equations cannot.” One of Adami’s current simulations is about cooperation and altruism. He is examining why cells help other cells when evolutionary theory suggests that every cell should look out for itself. He is studying colicin-producing bacteria
“It is analogous to reputation in humans,” Adami notes. “We are more willing to help those who have a good reputation for helping others.” Once communication is introduced to the simulation, cooperation is born. Cells use chemical signals to communicate their past behavior in cooperation transactions. Cooperation then becomes an evolutionary advantage. Computational testing supports this hypothesis, but it has not been tested with live cells. “To test these things requires sophisticated experiments and you have to find the right people to do them,” Adami says. “When I first arrived here and people were talking about what they’re doing, I kept thinking, ‘Yes, that’s what I need.’ This is where I need to be.”
His time away from his faculty position in California was only meant to last a year. Yet, Adami has decided to join MSU as a full-time professor in microbiology where he can work alongside the biologists, computer scientists, and engineers in BEACON. Adami first became interested in evolution during his post-doctoral studies when the director of a nuclear research facility gave him a paper on evolution inside of a computer. This stirred his passion of physics and evolution.
factor for understanding cooperation was communication.
Christoph Adami is a theoretical physicist who finds himself at home in microbiology.
According to Adami, evolution can be viewed as the evolution of information. In organisms, information is encoded as genes. The tools of physics, mathematics and computer simulations are well-suited for studying information evolution.
to understand this behavior since the bacteria live in colonies. When nonrelated bacteria colonize too much of the surrounding area, the colicin-producing bacteria explode and clear the area by spraying the colicin toxin. The only bacteria which survive are kin containing a colicin resistant gene.
Adami uses computational and theoretical methods of looking at evolution. He designed the AVIDA software which simulates an environment inside a computer where populations of computer programs can live and evolve.
Adami and his group are investigating what the colicin-producing bacteria gain through this process. The fitness of the kin group is maximized when the unrelated bacteria are destroyed, but the colicin-producing bacterium is dead. Adami and his team realized the missing
To test the cooperation hypothesis, Adami and his team have enlisted Ben Kerr from the University of Washington. Kerr is working with colicin-producing bacteria and will be testing Adami’s predictions in a living environment. “Directly connecting a physicist with biologists opens up a whole new realm of possibilities,” says Walt Esselman, chair of the department. “Our faculty are excited about the potential and our students are benefiting from the new opportunities this creates for research and learning.” So how does Adami feel about being a physicist in a department filled with biological scientists? “I feel like a kid in a candy store,” he says.
Michigan State University 5
Grant Targets Foodborne Illness
hannon Manning, assistant professor of microbiology, received a $2.4M grant from the USDA to develop strategies to reduce the amount of E. coli released by cattle which will decrease the incidence of foodborne illness in humans. The project will work to reduce cattle’s fecal “shedding” of shiga toxinproducing E. coli, called STEC. STEC is a leading cause of infections, but little is known about the factors influencing shedding from ruminant animals like cattle. Manning and her team of researchers will identify bacterial genotypes and epidemiological factors, determine how the bovine immune system responds to STEC, and compare the microbial communities in the gut of shedders and non-shedder animals. “These infections are a national concern, particularly during outbreaks when public health agencies are rapidly trying to identify the sources to prevent additional infections,” said Manning.
Manning’s laboratory studies the molecular epidemiology and evolutionary genetics of several infectious diseases including those caused by STEC and Streptococcus agalactiae. She describes her work as using molecular biology, population genetic, and evolutionary methods to answer questions about pathogenesis, emergence, virulence, evolution, and transmission of pathogens in human and animal populations. Manning has compared STEC and S. agalactiae and found them to be similar during phylogenetic and epidemiological analysis. This finding has led to several research projects including the work on reducing cattle’s fecal shedding of STEC. Additional projects include examining how infection with different pathogens alters the types of microbial communities present in the human intestine.
Improving Natural Killer Cells
ungjin Kim, assistant professor of microbiology, along with Elizabeth Gardner, associate professor of food science, were awarded a $2 million grant from the National Institutes of Health to study immune system responses to influenza. They are experimenting with improving natural killer (NK) cell response in older mice in order to find a way to control flu infections in vulnerable populations. Kim studies the development of NK cells in his lab at MSU. These cells are a type of lymphocyte and a crucial component of the immune system as they are the first responders to virusinfected cells. NK cells kill infected cells and limit the amount of virus which can spread through the body, especially the lungs, and cause damage.
Kim and Gardner have found that NK cells in older mice do not kill infected cells efficiently. This allows the flu virus to spread more rapidly and Sungjin Kim accumulate in the lungs during the first four days of infection. The older mice die during this period before the second wave of immunity can kick in. Their research suggests that NK cells are essential to control influenza early in the infection cycle and especially for older populations.
Department of Microbiology & Molecular Genetics
Environmental Exposures and Breast Cancer
irls eating a high-fat diet during puberty, even those who do not become overweight or obese, may be at a greater risk of developing breast cancer later in life, according to findings from research at MSU’s Breast Cancer and the Environment Research Center. Sandra Haslam, professor of physiology, and Richard Schwartz, professor of microbiology and associate dean in the College of Natural Science, are now expanding that research to continue studying the impact of prenatalto-adult environmental exposures that predispose women to breast cancer. They are part of the extended nationwide Breast Cancer and the Environment Research Program funded by the National Institute of Environmental Health Sciences and the National Cancer Institute. The work by Haslam and Schwartz builds on the team’s research that found the hormone progesterone activates genes that trigger inflammation in the mammary gland; that inflammation may be a key factor in increasing the risk of breast cancer. Haslam and Schwartz discovered that a high-fat diet during puberty produced many of the same effects seen as part of their progesterone research. The next phase of the study is working with the expanded national Breast Cancer and the Environment Research Program. Besides performing biomedical research, the new project also strives to communicate findings that can lessen the risk of breast cancer via awareness and avoidance of environmental risk factors.
New Center Builds Upon Research Strength in Human Microbiome STEC. HUS is a dangerous illness which can lead to kidney failure and death. Linda Mansfield is the principal investigator for ERIN. She points to the link between food-and-water-borne diseases and one of the most prevalent and important global health problems, diarrheal illnesses, as an example of the importance of ERIN’s research.
The three primary faculty involved in MSU’s Enterics Research Investigational Network are (left to right) Robert Britton, Linda Mansfield and Shannon Manning.
collaboration of MSU scientists are working to understand the microbes living in human intestines. While the trillions of microbes often form benign communities, the harmful microbes contribute to illnesses that kill millions of people each year across the world. The Enterics Research Investigational Network, Cooperative Research Center, or ERIN, is one of four centers focusing on enteric microbes funded by the National Institutes of Health. Sharon Manning is an assistant professor and her research focuses on how infection with different pathogens alters the type of microbes present in the intestine. “Our hope is to identify potentially beneficial microbes, microbial communities and/or microbial byproducts that can be used to prevent or treat disease,” Manning said. Manning’s lab studies the molecular epidemiology and evolutionary genetics of several infectious diseases including those caused by shiga toxin-producing E. coli (STEC) and Streptococcus agalactiae. STEC is a leading cause of infections in humans and is frequently spread through diarrhea.
Manning describes her work as using molecular biology, population genetic, and evolutionary methods to answer questions about pathogenesis, emergence, virulence, evolution, and transmission of pathogens in human and animal populations. Manning’s epidemiological analysis identified differences between genetic groups of STEC and the type of clinical disease reported. For example, hemolytic uremic syndrome (HUS) cases in Michigan were significantly more likely to be infected with certain strains of
“Our long-term goal is to develop new interventions and treatments for foodand water-borne diseases; we want to know what makes people more susceptible or more resistant to enteric diseases,” says Mansfield. Mansfield focuses on autoimmune diseases such as Guillain Barré syndrome and Miller Fisher syndrome which strike the nervous system and cause paralysis. These syndromes are linked to the bacteria Campylobacter. Robert Britton is also a key participant in the group. He is studying the interaction of microbial communities and antibiotics on pathogen emergence. ERIN is a component of the NIH’s Food and Waterborne Integrated Research Network and is funded by a 5-year, $7.3 million grant.
Book Honors Professor The late Thomas Whittam is being honored by his students and peers in a new book Population Genetics of Bacteria: a Tribute to Thomas S. Whittam. The publication uses Whittam’s research, projects, and ideas to explore the field of bacterial population genetics. The forty authors and two editors credit Whittam’s pioneering work in developing a statistical understanding of the abundance and distribution of genetic diversity in E. coli with inspiring them and their work. The STEC Center he founded is an outstanding collection of E. coli strains that supports the work of many experts in the field. Whittam was a mentor to many MSU faculty and served as the Hannah Distinguished Professor of Bacterial Evolution from 2001 until his death in 2008. The work being done with ERIN is an extension of Whittam’s research on the impact of E. coli in food safety and toxicology.
Michigan State University 7
DEPARTMENT OF MICROBIOLOGY & MOLECULAR GENETICS College of Natural Science 103 Natural Science Building East Lansing, MI 48824-1115
Join alumni and faculty for the
TIEDJE SYMPOSIUM ON MICROBIAL GENOMICS & ECOLOGY Honoring Professor Jim Tiedje as he celebrates his 70th birthday and featuring a day of scientific presentations from colleagues and alumni umni
Stay Connected! Saturday, October 29, 2011 Michigan State University For more details and to register: http://tiedjesymposium.mmg.msu.edu
Send us your career news, awards and updates.