Meet the Microbiologist

Joseph DeRisi is a Professor of Biochemistry and Biophysics at the University of California, San Francisco and a Howard Hughes Medical Institute Investigator. His research focuses on two distinct areas: malaria and new viral pathogen discovery.  Dr. DeRisi is this year’s recipient of the Eli Lilly and Company Research Award, granted in recognition of fundamental research of unusual merit in microbiology or immunology by an individual on the threshold of his or her career. Discovering new viral pathogens seems like exciting work, and DeRisi has lots of ideas for prospecting.  In one recent success with their viral microarray, his group recently helped identify the virus responsible for a devastating disease among rare parrots and other birds: proventricular dilatation disease, or PDD, has been recognized for 30 years, but veterinarians didn’t know the cause or how to control it.  Now that DeRisi’s group has pinpointed Avian Bornavirus as the culprit and sequenced its genome, therapies and control measures to help both captive birds and birds in the wild can’t be far behind.  In this interview, I asked Dr. DeRisi whether he’s interested in putting the microarray approach to virus discovery to work in uncovering the causes of some human illnesses, especially those diseases we suspect might be spread by viruses, but for which we’ve never found a virus responsible.  He has some very interesting ideas for where to start.  We also talked about his work on identifying the SARS virus, and a new approach in the ongoing fight against malaria.

Melanie Cushion holds down two jobs: she’s a research career scientist at the Veterans Administration Medical Center in Cincinnati, Ohio, and she’s also professor and associate chair for research in the department of internal medicine at the University of Cincinnati College of Medicine.  Dr. Cushion focuses her research on the fungus, Pneumocystis carinii, which is a harmless commensal for most people, but a deadly pathogen for others.  Pneumocystis carinii was shrouded in obscurity for many years until its fifteen minutes in the spotlight came in the 80’s, when, unfortunately, an outbreak of Pneumocystis pneumonia prefigured the AIDS epidemic.  Large numbers of previously healthy homosexual men in California became deathly ill with Pneumocystis pneumonia, and doctors knew something unusual (later found to be HIV) was going on.  Dr. Cushion says Pneumocystis pneumonia is an opportunistic infection: it strikes individuals with immune systems too weak to fend it off.  This explains why it was – and still is – a well-known sign that the patient is stricken with an active HIV infection or some other immune-suppressing disorder.  Dr. Cushion heads up the Pneumocystis genome project and she’s also looking into a new line of drugs called glucan synthase inhibitors, which have a profound effect on Pneumocystis’s life cycle and may offer new insights into managing the pathogen. In this interview, I talked with Dr. Cushion about some of the more surprising results to come out of her genomics work, why Pneumocystis is a tough nut to crack in the laboratory, and about why she’s not giving her young investigator award back to the Society of Protozoologists any time soon.

Ian Orme is a professor in the Department of Microbiology, Immunology, and Pathology at Colorado State University, and his research focuses on the immune response to tuberculosis (TB) – a bacterial disease that most often infects the lungs. He's speaking at the American Society for Microbiology's Conference for Undergraduate Educators (ASMCUE). In the U.S., TB seems like a thing of the past. Here, public health measures and medical care have all but wiped out the threat from this infection. But worldwide, the WHO says there were 9.2 million new TB cases in 2006 alone, and each person with TB infects an average of 10 to 15 people with the TB bacterium every year. These are just some of the reasons Dr. Orme is delivering a talked titled “Tuberculosis: Why Now Is a Good Time to Leave the Planet” at ASMCUE. He admits leaving the planet isn’t a practical suggestion, but he wants to raise awareness of the disease and he’s not afraid to stir the pot a little. Orme and his group not only study the immune responses to TB bacteria, they’re also following a number of different avenues for developing new vaccines and improving the existing vaccine, BCG (bacille Calmette-Guérin). In this interview, I talked with Dr. Orme about his vaccine work, why he thinks latent TB bacteria aren’t really latent, and how he sometimes feels like the wild-haired radical, cat-calling from the corner of the lecture hall.

Parisa Ariya is a professor in the Department of Atmospheric and Oceanic Sciences and the Chemistry Department at McGill University in Montreal.  Dr. Ariya works mostly in atmospheric chemistry, but she’s also done a good deal of work with bioaerosols and airborne microorganisms.  She’ll deliver a talk at the ASM General Meeting in May titled Bioaerosols: Impact on Physics and Chemistry of the Atmosphere. Bioaerosols – microscopic clumps of microorganisms and organic debris – arise through any of a number of mechanisms.  The scientific community has come full circle on the idea of microorganisms in the atmosphere, according to Dr. Ariya.  Back in the early days of microbiology it was widely recognized that the air is full of living, breathing microbes, but once our understanding of atmospheric chemistry and physics matured, the roles of microbes in atmospheric processes were marginalized.  Thanks, in part, to Dr. Ariya’s work, the activities and functions of bioaerosols are getting new attention.  We now know cells in bioaerosol particles can actively metabolize materials at interfaces, and Dr. Ariya says some of her future work will look into the details of these transformation processes and how they impact the atmosphere. In this interview, Dr. Merry Buckley talks with Dr. Ariya about how bioaerosols are formed, what they’re doing, and why it isn’t a good idea to use bioaerosols to manage the weather.

Jeff Bender is a professor of veterinary public health at the University of Minnesota, and his research interests lie in the intersection of animal health and human health, including animal-borne diseases of humans, food safety, and antibiotic resistant pathogens in animals.  Dr. Bender will speak on “Methicillin-resistant Staphylococcus aureus ( MRSA) in Veterinary Practice” at the American Society for Microbiology’s General Meeting in Philadelphia this May. To a microorganism, vertebrates can all look pretty similar.  Dr. Bender’s work focuses on pathogens that can make themselves at home in both human bodies and the bodies of our pets and livestock.  Outbreaks of bacterial illnesses from meat products are well publicized these days, but the pathogens we have in common with animals don’t just travel in one direction.  We humans can pass organisms and diseases to our animals, too.  Dr. Bender says pets treated at veterinary clinics, for example, have come down with painful MRSA skin infections they picked up from their owners.  Fluffy might become a temporary reservoir of MRSA in your home – capable of reinfecting you and your family, but the good news is that she probably won’t be a long term carrier of the bacterium. In this interview, Dr. Merry Buckley asks Dr. Bender about MRSA in pets, whether farmers often get sick from animal-borne diseases, and whether he thinks it’s a good idea to “go organic” when shopping for food.

Jo Handelsman is a professor at the University of Wisconsin, where she’s a member of the Department of Plant Pathology and chair of the Department of Bacteriology. Dr. Handelsman’s research focuses on microbial communities – their composition, how they’re structured, and how they work. Thanks to her work to improve the quality of undergraduate education, Dr. Handelsman is this year’s recipient of the American Society for Microbiology’s Carski Foundation Undergraduate Teaching Award. Dr. Handelsman has been at the cutting edge of microbial science for years. After a long time spent studying the teeming communities of microorganisms that dwell in soil, Handelsman has pared down her focus to some arguably simpler neighborhoods: the guts of insects. Handelsman applies molecular methods to identify the strains and genes present in bug guts and combines this knowledge with other information about these environments to learn what these communities might be doing. Handelsman also takes a particular interest in science education, and along with her colleagues Sarah Miller and Christine Pfund, she recently co-authored Scientific Teaching, a book that outlines a dynamic research- and results-driven approach to teaching college-level science. In Dr. Merry Buckley's interview with Dr. Handelsman, they discuss about why microbiologists have a responsibility to educate almost everyone, why bacterial communities in the guts of gypsy moths might need genes for antibiotic resistance, and why and how bacteria inside of insects communicate. They also talk about the underrepresentation of women in academic research appointments and about how universities need to change to make these jobs both more available and attractive for all those brainy women who won’t (or can’t) make the jump from graduate school to academic research.

David Knipe is the Higgins Professor of Microbiology and Molecular Genetics at Harvard Medical school. A virologist, Dr. Knipe focuses his research efforts on the herpes simplex virus 2 (HSV-2) – the virus we have to thank for genital herpes. An astonishing 20% of Americans have been infected with HSV-2, and whether they’ve had a recognizable outbreak of sores or not, they can still carry the virus. Once you contract the HSV-2 it lays low in your nerve cells, waiting for the right moment to create watery blisters that eventually burst and release more virus particles. Dr. Knipe is interested in how the cells lead these two, very different lives: quiet and quiescent inside the nerve cell and loud and lytic in the epithelium on the surface of the body. Genital herpes is no picnic, but the effects of HSV-2 infection are worst in people with depressed immune systems and in newborns; babies who pick up the virus during birth may suffer from neurological damage, brain damage, or even death. There is no cure for genital herpes, and no means of getting rid of HSV-2, only ways of managing outbreaks. But there is some hope of relief; Dr. Knipe’s lab has developed a vaccine that will enter the trial phase soon. In this interview, I asked Dr. Knipe about how he got interested in viruses, about the vaccine he’s developed and who could hope to benefit from it, and why it’s taken science so long to develop a vaccine for this extremely common disease.

Dr. Andrew Knoll is the Fisher Professor of Natural History in Harvard University’s Department of Organismic and Evolutionary Biology, where he studies ancient life, its impacts on the environment, and how the environment, in turn, shaped the evolution of life.  In recognition of the 200th anniversary of Charles’ Darwin’s birth and the 150th anniversary of the first printing of his book, “On the Origin of Species”, the American Society for Microbiology has invited Dr. Knoll to deliver the opening lecture, titled “Microbes and Earth History,” at the society’s general meeting in Philadelphia this year. Before the dinosaurs, before trees and leaves, before trilobites, there were microbes.  Vast, slimy layers of them covered the rocks and peppered the seas of the harsh, alien planet we now call Earth.  Those slimy cells were our ancestors, and they played a defining role in changing that once-barren moonscape into the world we see today: a planet covered with diverse, striving life, topped by an oxygen-rich atmosphere.  Dr. Knoll says he puts on his paleontologist’s hat and studies the fossil record to learn more about this ancient life, then he dons his geochemist’s hat to reconstruct Earth’s environmental history from the chemical signatures he finds in ancient sedimentary rocks.  He weaves these two stories together to figure out how life has transformed the planet and how the planet has influenced the course of evolution. In this interview, I talk with Dr. Knoll about what early earth must have looked like, his involvement with the Mars rover project, and how intelligent design concepts may well belong in high school curricula, but not in the context of science class.

Roberto Kolter is a professor of Microbiology andMolecular Genetics at Harvard’s Medical School.  Dr. Kolter’s research interests are broad, but he says his eclectic program boils down to an interest in the ecology and evolution of microbes, bacteria in particular, and on how these forces operate at the molecular level. Although he’s worked in a number of different systems, lately Dr. Kolter is spending a lot of time with Bacillus subtilis, a modest little bacterium that doesn’t get the headlines of a wicked pathogen like Salmonella or a useful industrial workhorse like yeast.  What it lacks in notoriety,  B. subtilis makes up for in usefulness.  According to Dr. Kolter, B. subtilis is an important source of industrial enzymes (as in laundry detergent) and, as a bacterial model, a prolific source of information on how some bacteria make spores and other diverse cell types.  This ability to form different kinds of cells is intriguing to Dr. Kolter: B. subtilis cells can wear any of a number of different hats, depending on what is needed at any given moment.  From spores to swimming cells to cells that wage chemical warfare on their neighbors, B. subtilis can do it all.  Dr. Kolter and his colleagues are looking at the how and the why of this multiplicity. In the interview, Dr. Merry Buckley talks with Dr. Kolter about what he finds interesting about B. subtilis, why we should start thinking about bacteria as multicellular organisms, and how he got involved in producing a book of poetry (poetry about microbes, that is). Dr. Kolter also provided the photography for the book Germ Stories by Arthur Kornberg. To see a full description and pricing details, click the ASM estore and pick up your copy today.

Dr. Ellen Jo Baron is a professor of pathology and director of clinical microbiology at Stanford University’s medical center in Palo Alto, California.  A co-author of the authoritative Manual of Clinical Microbiology, Dr. Baron and her staff in the clinical lab evaluate and advise in the development of new diagnostic technologies.  Dr. Baron has also volunteered her time as a microbiology advisor in numerous hospitals and clinics in developing countries since 1996. In a hospital, you have to be able to diagnose infections in order to treat patients, but hospitals in the developing world that are forced to get along with inadequate and ill-equipped microbiology labs have to treat infectious disease blindly, without full knowledge of which organism is to blame and which drugs will be most effective.  These missteps cost lives.  Dr. Baron, who normally works in a modern, fully-equipped western hospital, travels to hospitals and clinics in places like Cambodia and Nepal to train staff and organize clinical microbiology labs.  She says it’s not always feel-good work for her: cumbersome bureaucracy and lack of money and equipment are constant challenges.  But experiencing other cultures and getting out of her comfort zone help make the work rewarding. In this episode, Dr. Merry Buckley talks with Dr. Baron about her work at home and abroad, the kinds of problems she faces in under-resourced labs, and about how, as a result of her work in the developing world, she now knows more about sheep and goats than she ever really wanted to know.