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Meet the Scientist Podcast by Carl Zimmer

Meet the Scientist Podcast

by Carl Zimmer

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At Meet the Scientist, we want to reveal more about scientists, the work they do, and what makes them tick. We?ll ask them what they're up to now and what's next. How is the science moving forward to solve some of the intractable problems of our times? What keeps them going in a tough, competitive field? What do they see for the future of research, education, and training? We hope to show you a glimpse of what scientists are really like and what's going on in cutting-edge research today. For more information please visit www.microbeworld.org. For questions and/or feedback please email ccondayan@asmusa.org.

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MTS64 - Martin Blaser - Save Our Endangered Germs

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Dec 29, 2010

In this podcast, I speak to Martin Blaser, Frederick H. King Professor of Internal Medicine and Chairman of the Department of Medicine and Professor of Microbiology at the New York School of Medicine. Blaser studies Helicobacter pylori, bacteria that live in the stomachs of billions of people. Blaser has shown that H. pylori has a strange double life inside of us. On the one hand, it can cause ulcers and gastric cancer. On the other hand, it can protect us from diseases of the esophagus, allergies, asthma, and perhaps even obesity. We're now eradicating H. pylori with antibiotics and other luxuries of modern life; Blaser thinks we ought to bring it back--but keep it on a tight leash.

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MTS63 - Jeff Gralnick - I Sing the Microbe Electric

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Dec 16, 2010

All life hums with electricity, from our heartbeats to the electrons that flow to the oxygen we breathe.But some bacteria are electricians par excellence, generating electric currents in the soil and water.

In this podcast, I talk to microbe-electricity expert Jeff Gralnick of the University of Minnesota about the biology behind these currents, and how engineers may be able to harness it to power technology.

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MTS62 - Jessica Green - The Living Air

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Tue, Nov 23, 2010

In this podcast I talk to Jessica Green of the University of Oregon about aerobiology: the science of life in the air.

We live in an invisible ocean of life, with millions of microbes swarming around us. Microbes can live many miles high in the upper atmosphere, and they may actually be able to feed and grow in clouds. Green and I talk not just about high-altitude aerobiology, but about the microbes we share our homes and offices with, and how better understanding them can help our health.

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MTS61 - Charles Bamforth - Beer: Eight thousand years of biotechnology (39.5 min.)

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Nov 04, 2010

In this podcast, I talk to Charles Bamforth of the University of California, Davis, about the surprisingly complex chemistry of beer, and the pivotal role microbes play in making it happen.

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MTS60 - Thomas Scott - The Bone-Breaking Virus (29.5 min.)

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Oct 20, 2010

In this podcast I talk to Thomas Scott of the University of California, Davis, about dengue fever, a disease that's on the rise. Spread by mosquitoes, it can make you feel as if your bones are broken and leave you exhausted for months. In more serious cases, people suffer uncontrollable bleeding and sometimes die. Dengue is expanding its range, and is even making incursions into the United States. Scott and I talk about what scientists know and don't know yet about dengue, and what the best strategy will be to drive the virus down.

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MTS59 - Charles Ofria - Digital Life

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Oct 06, 2010

In this podcast I talk to Charles Ofria, a computer scientist at Michigan State University.

Ofria and his colleagues have created a program called Avida in which digital organisms can multiply and evolve. They are studying many of evolution's deepest questions, such as how complexity evolves from simplicity and why individuals make sacrifices for each other. The evolution unfolding in Avida is also yielded new software that can run robots and sensors in the real world.

Bonus Content includes:

Avida Movie

In this movie, we started with a normal Avida organism in the middle of the population and let it grow for a while before injecting a highly-virulent parasite into the middle.  The hosts are all colored with shades of blue and the parasites are shades of red.

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MTS58 - David Baker - Crowdsourcing Biology

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Sep 23, 2010

In this podcast I spoke to David Baker, a professor of biochemistry at the University of Washington. Baker and his colleagues study how proteins fold, taking on the complex shapes that make our lives possible.

It turns out that protein folding is a fiendishly hard problem to solve, and even the  most sophisticated computers do a poor job of solving it. So Baker and his colleagues have enlisted tens of thousands of people to play a protein-folding game called Foldit. I talked to David Baker about the discoveries they've made through crowdsourcing, and the challenges of getting 57,000 co-authors listed on a paper.

Additional Resources:



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MTS57 - Forest Rohwer - Curing the Corals

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Sep 01, 2010

It never occurred to me that the human body and a coral reef have a lot in common--until I spoke to Forest Rohwer for this podcast. Rohwer is a microbiologist at San Diego State University, and he studies how microbes make coral reefs both healthy and sick. Just as we are home to a vast number of microbes, coral reefs depend on their own invisible menagerie of algae and bacteria to get food, recycle waste, and fend off invaders. But as Rohwer writes in his new book, Coral Reefs in the Microbial Seas, we humans have thrown this delicate balance out of kilter, driving the spread of coral-killing microbes instead.

Additional Reading:

Viral communities associated with healthy and bleaching corals.
The lagoon at Caroline/Millennium atoll, Republic of Kiribati: natural history of a nearly pristine ecosystem.
Metagenomic analysis of stressed coral holobionts.

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MTS56 - Susan Golden - Clocks for Life

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Aug 18, 2010

In this podcast, I talk to Susan Golden, the co-director of the Center for Chronobiology at the University of California at San Diego.

We talked about Golden's research into time--in particular, how living things know what time it is. While you may have heard of our own "body clock" that tracks the 24-hour cycle of the day, it turns out that some bacteria can tell time, too. Golden has discovered how evolution has produced a molecular clock inside microbes far more elegant than any manmade timepiece.

Additional Reading:

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MTS55 - Nancy Moran - The Incredible Shrinking Microbe

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Aug 04, 2010

How many genes can a species lose and still stay alive? It turns out, bacteria can lose just about all of them!

In this podcast, I talk to Nancy Moran of Yale University about her fascinating work on the microbes that live inside insects such as aphids and cicadas. After millions of years, they have become stripped down creatures that are revealing some profound lessons about how superfluous most genes are--at least if you live inside a host.

Recent Publications:

Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host

Symbiosis and insect diversification: an ancient symbiont of sap-feeding insects from the bacterial phylum Bacteroidetes

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MTS54 - Carl Bergstrom - The Mathematics of Microbes

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jul 14, 2010

In this podcast I talk to Carl Bergstrom of the University of Washington about the mathematics of microbes.
Bergstrom is a mathematical biologist who probes the abstract nature of life itself. We talk about how life uses information, and how information can evolve. But in Bergstrom's hands, these abstractions shed light on very real concerns in medicine, from the way that viruses jam our immune system's communication systems to to the best ways to fight antibiotic resistance.
Mapping Change in Large Networks [html] [pdf]
The transmission sense of information [pdf]
Dealing with deception in biology [pdf]

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MTS53 - Bonnie Bassler - The Bacterial Wiretap

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Jul 01, 2010

In this podcast I talk to Bonnie Bassler, a professor at Princeton and the president-elect of the American Society for Microbiology.

Bassler studies the conversations that bacteria have, using chemicals instead of words, Her research is not only helping to reveal how bacteria work together to make us sick, but also how we might interrupt their dialogue in order to cure infections.

Related Projects:

Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell.

Information processing and signal integration in bacterial quorum sensing.

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MTS52 - Mitchell Sogin - Expeditions to the Rare Biosphere

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Jun 17, 2010

In this podcast, I talk to Mitchell Sogin, the Director of the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory in Wood's Hole, Massachusetts.

Dr. Sogin is one of the leaders of an ambitious project to survey the microbes of the ocean--which total over 36,000,000,000,000,000,000,000,000,000,000 cells. Using the latest DNA-sequencing technology, Dr. Sogin and his colleagues are cataloging microbes from all over the world, and are discovering a genetic diversity in the microbial world far exceeding anyone's expectations. 

Dr. Sogin explained how most species they find only exist in small numbers, while a minority of species dominate their samples. Dr. Sogin is investigating how this "rare biosphere" changes the way we understand how the ocean's ecosystems work.

Related Projects:

International Census of Marine Microbes

Woods Hole Center for Oceans and Human Health

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MTS51- James Liao - Turning Microbes into Fuel Refineries

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jun 02, 2010

In this podcast I talk to James Liao, a professor in the Department of Chemical and Biomolecular Engineering at UCLA. I spoke to Dr. Liao about his research into engineering microbes to make fuel.

Today, we get most of the fuel for our cars out of the ground. It's a process fraught with dangerous consequences, from the oil spill in the Gulf of Mexico to the rise in global temperatures thanks to greenhouse gases. Dr. Liao is among a growing number of scientists who think that microbes can help us out of this predicament.

We talked about the attraction of microbe-derived fuels, and the challenges of getting bacteria to turn air, water, and sun into something that can power your car.

Selected Publications

Atsumi, S.; T. Hanai and J.C. Liao (2008) Non-Fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels, Nature, 451:86-89.

Atsumi,S.; Higashide, W.; and Liao, J.C. (2009) Direct recycling of carbon dioxide to isobutyraldehyde using photosynthesis, Nat Biotechnol, 27, 1177-1180

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MTS50.5 - The Making of the Meet the Scientist Podcast

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, May 21, 2010

To mark the celebration of Microbeworld's 50th episode of the Meet the Scientist podcast, we created a time lapse video that shows exactly what it takes to produce a single episode of the show.

We hope you enjoy this behind the scenes look and we thank you for listening week after week. Cheers, to another 50 episodes!

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MTS50 - R. Ford Denison - Darwin on the Farm

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, May 19, 2010

In this podcast, I talk to R. Ford Denison of the University of Minnesota. Denison is an evolutionary biologist who's interested in how to make agriculture better. The ways in which plants thrive or fail are shaped by their evolutionary history, as well as the evolution that unfolds every planting season.

We're most familiar with the evolution of resistance to pesticides in insects and to herbicides in weeds. But evolution has many other effects on farms. For example, many important crop plants, like soybeans, cannot extract nitrogen from the atmosphere on their own. They depend instead on bacteria that live inside their roots.

In exchange for fixed nitrogen, the bacteria get nutrients from the plants. It may seem like a happy case of cooperation, but the evolution of cooperation always runs the risk of cheating and deception. How plants and bacteria come to a compromise is a remarkable story that Denison and his colleagues are now documenting.

Selected Publications

Denison, R.F. 2010. Darwinian agriculture: where does nature's wisdom lie? Book in preparation for Princeton University Press.

Ratcliff, W.C., P. Hawthorne, M. Travisano, R.F. Denison. 2009. When stress predicts a shrinking gene pool, trading early reproduction for longevity can increase fitness, even with lower fecundity. PLoS One 4:e6055

Kiers E. T., R.A. Rousseau, S. A. West, and R. F. Denison. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425:78-81.

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MTS49 - Irwin Sherman - The Quest for a Malaria Vaccine: The First Hundred Years

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, May 05, 2010

In this podcast, I talk with Irwin Sherman, professor emeritus at the University of California at Riverside, about the century-long quest for a vaccine against malaria.

Scientists have been trying to make a vaccine for the disease almost since the discovery of the parasite that causes malaria. Yet decade after decade, they've encountered setbacks and failures. We talked about why it's so hard to make a malaria vaccine, and how likely it is that scientists will ever be able to do so in the future.

If you want to find out more about this long-running saga, check out Sherman's new book, The Elusive Malaria Vaccine: Miracle or Mirage.

About the Book

Chronicling a 100-year quest, this book tells the fascinating story of the hunt for the still-elusive malaria vaccine. Its clear, engaging style makes the book accessible to a general audience and brings to life all the drama of the hunt, celebrating the triumphs and documenting the failures. The author captures the controversies, missteps, wars of words, stolen ideas, and clashes of ego as researchers around the world compete to develop the first successful malaria vaccine.

The Elusive Malaria Vaccine: Miracle or Mirage? is based on author Irwin W. Sherman’s thorough investigation of the scientific literature as well as his first-hand interviews with today’s pioneers in malaria vaccine research. As a result, the book offers remarkable insights into the keys to a successful malaria vaccine and the obstacles hindering its development.


Malaria is one of humankind’s greatest killers, currently afflicting some 300 to 500 million people. Moreover, malaria infections have begun to spread and surge in places previously free from the disease. With the book’s easy-to-follow coverage of such topics as immunity, immunology, recombinant DNA, and monoclonal antibodies, readers gain a new understanding of the disease itself, the importance of microbe hunters, and the need for responsible leadership to face the challenges that lie ahead in the battle against malaria.


Other Publications from Dr. Sherman

Twelve Diseases That Changed Our World

The Power of Plagues

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MTS48 - Keith Klugman - Pneumonia: The Hidden Giant

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Apr 21, 2010

In this podcast I talk to Keith Klugman, William H. Foege Chair of Global Health at Emory University.

Dr. Klugman studies the disease that is the number one killer of children worldwide. If you guessed malaria or AIDS, you’d be wrong. It’s pneumonia. Two million children under five die every year from it every year--one child every 15 seconds.


Dr. Klugman and I spoke about his research on how pneumonia causes so much devastation, its hidden role in the 50 million deaths in the 1918 flu pandemic, and how a new pneumonia vaccine can stop the disease in its tracks. For more information on pneumonia and how we can all help fight it, visit the World Pneumonia Day web site.

Dr. Klugman's recent publications:

A role for Streptococcus pneumoniaein virus-associated pneumonia (pdf)

Levo?oxacin-Resistant Invasive Streptococcus pneumoniae in the
United States: Evidence for Clonal Spread and the Impact of
Conjugate Pneumococcal Vaccine (pdf


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MTS47 - Peter Daszak - Stalking the Wild Microbe

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Apr 07, 2010

Dr. Peter Daszak is a disease ecologist and President of the Wildlife Trust, an international organization of scientists dedicated to the conservation of biodiversity. He is a leader in the field of conservation medicine and is well known for uncovering the wildlife origin of the SARS virus. Dr. Daszak also identifed the first case of a species extinction caused by a disease and has demonstrated a link between global trade and disease emergence via a process called "pathogen pollution."

In this interview I ask Dr. Daszak about the threat new pathogens pose to endangered species and go into detail about his discovery that chytridiomycosis, a fungal disease caused by the chytrid Batrachochytrium dendrobatidis, is responsible for global amphibian population declines. Dr. Daszack also discusses a unique study that exposes how the W.H.O. might better use their resources when faced with new pathogens such as the kind we've seen with the recent outbreak of the H1N1 virus. We also explore how pathogens of animals have the ability to evolve into human diseases like flu and HIV.

Links to research discussed in this episode:

Infectious disease and amphibian population declines (.pdf)

Emerging infectious diseases of wildlife--threats to biodiversity and human health

Wildlife Trust page about SARS

Monitoring the Deadly Nipah Virus

Assessing the Impacts of Global Wildlife Trade

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MTS46 - Curtis Suttle - It's a Virus World and We Just Live On It

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Mar 24, 2010

In this podcast I talk to Curtis Suttle, a professor and associate dean at the University of British Columbia.Suttle studies the diversity and population of viruses across the entire planet. He has helped show that viruses are by far the most common life forms on the planet. They also contain most of the genetic diversity of life, and they even control how much oxygen we have to breathe. I talked to Suttle about coming to terms with the fact that we live on a virus planet, and how hard it is to find a place on Earth that's virus-free--even two miles underground. 

Links to Curtis Suttle and his work.

Curtis Suttle's Labatory Website

A detailed listing of Curtis Suttle's publications

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MTS45 - James Collins - Engineering Life: The Past and Future of Synthetic Biology

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Mar 04, 2010

In this podcast, I talk to James Collins, an investigator at the Howard Hughes Medical Institute and a professor at Boston University.

Ten years ago Collins helped launch a new kind of science called synthetic biology. I talked to Collins about the achievements of synthetic biology over the past decade, such as engineering E. coli that can count, and about the future of synthetic biology--from using bacteria to make fuel to reprogramming the bacteria in our guts to improve our health.

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MTS44 - Michael Worobey - In Search of the Origin of HIV and H1N1's Hidden History

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Feb 18, 2010

In this episode, I talk to Michael Worobey, an associate professor at the University of Arizona.

Worobey is virus detective, gathering clues about how some of the world's deadliest pathogens have emerged and spread across the globe. Worobey and I talked about the harrowing journeys he has made in search of the origin of HIV, as well as the round-the-clock data-processing he and his colleagues used to discover the hidden history of the new H1N1 flu strain.

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MTS43 - Rob Knight - The Microbes That Inhabit Us

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Feb 03, 2010

In this episode, I speak to Rob Knight, an assistant professor in the Department of Chemistry and Biochemistry at the University of Colorado, Boulder.

Knight studies our inner ecology: the 100 trillion microbes that grow in and on our bodies. Knight explained how hundreds of species can coexist on the palm of your hand, how bacteria manipulate your immune system and maybe even your brain, and how obesity and other health problems may come down to the wrong balance of microbes.

Links to studies mentioned in this episode:

Ruth Ley and Peter Turnbaugh's studies on obesity in Jeff Gordon's lab:
Obesity alters gut microbial ecology.
Microbial ecology: human gut microbes associated with obesity.
An obesity-associated gut microbiome with increased capacity for energy harvest.
A core gut microbiome in obese and lean twins.
Julie Segre's studies of the skin:
A diversity profile of the human skin microbiota.
Topographical and temporal diversity of the human skin microbiome.
Chris Lauber and Elizabeth Costello's studies of human-associated body habitats (in Noah Fierer's and Rob Knight's lab):
The influence of sex, handedness, and washing on the diversity of hand surface bacteria.
Bacterial community variation in human body habitats across space and time.
Jeremy Nicholson's studies of the metabolome:
Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism.
Cathy Lozupone's study of global microbial diversity (in Rob Knight's lab), and confirmation of the patterns in archaea by Jean-Christophe Auguet:
Global patterns in bacterial diversity.
Global ecological patterns in uncultured Archaea.
Ruth Ley and Cathy Lozupone's study integrating gut-associated and environmental bacteria:

Worlds within worlds: evolution of the vertebrate gut microbiota.

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MTS42 - Julian Davies - The Mysteries of Medicine's Silver Bullet

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jan 20, 2010

In this episode I speak to Julian Davies, professor emeritus in the Department of Microbiology & Immunology at the University of British Columbia.

Dr. Davies is one of the world's experts on antibiotics. I talked to Davies about how the discovery of antibiotics changed the course of modern medicine, and how we now face a growing threat from the evolution of antibiotic-resistant bacteria. We also talked about some enduring mysteries about antibiotics.

Most of us think of antibiotics as a way to kill microbes. But the fact is that microbes make antibiotics naturally, and for them, these molecules may not be lethal weapons. They may actually be a way to talk to other microbes.

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MTS41 - Sallie Chisholm - Harvesting the Sun

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jan 06, 2010

In this episode I speak to Sallie "Penny" Chisholm, the Lee and Geraldine Martin Professor of Environmental Studies at MIT. Dr. Chisholm studies photosynthesis—the way life harnesses the energy of the sun. Plants carry out photosynthesis, but so do microbes in the ocean. Dr. Chisholm studies the most abundant of these photosynthetic microbes, a species of bacteria called Prochlorococcus.  There are a trillion trillion Prochlrococcus on Earth. Dr. Chisholm researches these microbial lungs of the biosphere, and how they produce oxygen on which we depend.

Along with her scientific research, Dr. Chisholm is also the author of a new children's book, Living Sunlight: How Plants Bring The Earth To Life.

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MTS40 - John Wooley - Exploring the Protein Universe

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Dec 23, 2009

John Wooley is Associate Vice Chancellor of Research and Professor of Chemistry-Biochemistry and of Pharmacology at the University of California San Diego. Wooley is a leader in the young field of metagenomics: the science of gathering vast numbers of genes from the oceans, soils, air, and the human body.

A generation ago biologist knew the sequences of a few thousand genes. Since then that figure has jumped to several million genes and it's only going to continue to leap higher in years to come. This wealth of data is allowing scientists to get answers to fundamental questions they rarely even asked a generation ago.

They're starting to understand how thousands of species of microbes coexist in our bodies. They're investigating how hundreds of genes work together inside a single cell and they're starting to get a vision of the full diversity of the billions of proteins that life produces, what scientists sometimes call the protein universe.

John Wooley has been at the center of this revolution, investigating some of these new questions and leading pioneering projects such as CAMERA, the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis, to organize the unprecedented amount of data that scientists have at their disposal so that they can master that data rather than drown in it.

In this episode I spoke to Wooley about how metagenomics has revolutionized research on everything from marine ecology to human health, and how he and his colleagues cope with an influx of data on millions of new genes.

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MTS39 - Paul Turner - Pandemic in a Petri Dish

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Mon, Dec 07, 2009

In this episode I talk with Paul Turner, an associate professor of ecology and evolutionary biology at Yale University.

2009 saw the emergence of a new strain of H1N1 flu. Scientists soon determined that the virus had leaped from pigs to humans and then spread to millions of people.

When viruses make this kind of leap it's a reason to worry. In 1918 when a strain of flu leapt from birds to humans, 50 million people died in a matter of months. So far the new H1N1 flu strain is behaving like a relatively ordinary flu. Still even ordinary flu is a matter of serious concern. Over 4,000 people in the US alone have died from the new H1N1 flu strain and scientists can't say for sure what it would take to turn this new strain into a global killer.

It's a sobering reminder of how mysterious virus evolution remains. Over the past century a number of viruses have made the leap from animal host to humans including SARS and HIV and scientists worry that the next great plague may be a virus that we don't even know about yet.

Paul Turner is learning how new viruses emerge by watching them evolve in his lab. Fortunately the viruses he studies don't make you sick. Instead they attack E-coli and other single celled hosts. But these viruses are teaching Turner and his colleagues about some of the fundamental rules that govern how viruses evolve to attack new hosts. Turner hopes that what he and his colleagues learn about those rules may help future generations of scientists fight against the next generation of viruses that can make us sick.

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MTS38 - Jonathan Eisen - An Embarrassment of Genomes

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Nov 05, 2009

Jonathan Eisen is a professor at the University of California, Davis Genome Center. Over the course of his career, he has pioneered new ways of sequencing microbial genomes and analyzing them.

I talked to Eisen about some of the weirdest creatures he's studied, such as bacteria that only live on the bellies of worms at the bottom of the ocean, and how we may be able to exploit their genomes for our own benefit. We also discussed the new movement for open access to scientific literature, a subject that's a particular passion of Eisen, who is academic editor in chief at the open-access journal PLOS Biology.

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MTS37 - Hazel Barton - Cave Dwellers

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Oct 23, 2009

Hazel Barton is the Ashland Professor of Integrative Science at Northern Kentucky. She explores some of the world's most remote caves to study the remarkable diversity of microbes that thrive in their dark rececesses. I spoke to Barton about how she first became captivated by these bizarre organisms, what it's like to do delicate microbiology when you're hip-deep in mud, and why she wants to explore caves on Mars in search of Martians.


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MTS36 - Dennis Bray - Living Computers

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Oct 09, 2009

Dennis Bray is an active professor emeritus in both the Department of Physiology and Department of Neuroscience at the University of Cambridge. He studies the behavior of microbes--how they "decide" where to swim, when to divide, and how best to manage the millions of chemical reactions taking place inside their membranes. For Bray, microbes are tiny, living computers, with genes and proteins serving the roles of microprocessors.

In this interview, I talked with Bray about his provocative new book, Wetware: A Living Computer Inside Every Cell.

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MTS35 - Michael Cunliffe - The Ocean's Living Skin

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Sep 11, 2009

Michael Cunliffe is a microbiologist in the Department of Biological Sciences at the University of Warwick in England. He studies the microbes that live in the thin layer of water at the very surface of the ocean. His research is shedding light on an ecosystem that's both mysterious and huge, spanning three-quarters of the surface of the planet.

In this interview, I talked with Cunliffe about the discovery of this sea-surface ecosystem, and the influence it has over the Earth's climate.

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MTS34 - Pratik Shah - Combatting Pathogens with Polyamines

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Aug 28, 2009

Pratik Shah is a graduate student in the Department of Microbiology at the University of Mississippi Medical Center in Jackson, and he’s a 2009 recipient of ASM’s Raymond W. Sarber award, granted to recognize students for research excellence and potential.

His research focuses on polyamines and polyamine biosynthesis and transport systems in Streptococcus pneumoniae.  He’s studying polyamines with the goal of finding potential targets for pneumococcal vaccines and prophylactic interventions against pneumococcal disease.  

In this interview, I talked with Pratik about why polyamines may hold the key for new ways to combat pathogens, his plans for the future, and about advice he would give to young people considering grad school.

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MTS33 - Abigail Salyers - The Art of Teaching Science

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Aug 13, 2009

Abigail Salyers is a Professor of Microbiology and the G. William Arends Professor of Molecular and Cell Biology at the University of Illinois at Urbana-Champaign, and her research focuses on the ecology of microorganisms in the human body and the comings and goings of antibiotic resistance genes, particularly genes in Bacteroides species.  Dr. Salyers is ASM’s 2009 Graduate Microbiology Teaching Awardee. 

If you’ve ever tried teaching or mentoring, you know it’s not always easy, but for an eminent scientist, teaching at the undergraduate or graduate level must be incredibly difficult.  After all, once you reach a certain level of knowledge in any field, it can be hard to relate your knowledge to people who know relatively little about it.  Dr. Salyers has tackled 100-level biology courses with as many as 300 students, taught one-on-one at the lab bench, and been an instructor at an intensive summer course in microbial diversity, all while rising to the top of her field in research. 

In this interview, I talked with Dr. Salyers about the most influential teacher in her own life (you might be surprised to learn who that is), about whether antibiotic resistance is getting the kind of play it deserves, and about why the baboon vagina is an interesting study system.

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MTS32 - Arthur Guruswamy - Mycobacterial and Fungal Pathogens

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jul 29, 2009

Arthur Guruswamy is a clinical microbiologist in Virginia’s Department of General Services Division of Consolidated Laboratory Services and the winner of ASM's Scherago-Rubin Award in recognition of an outstanding, bench-level clinical microbiologist.  His particular interest lies in mycobacterial and fungal diseases, including tuberculosis. 

In his work, Mr. Guruswamy places a lot of emphasis on helping others.  A while back, he traveled to his native Sri Lanka to train clinic staff in the use of a rapid, low tech method for identifying cases of tuberculosis.  Using this method has probably saved many lives, since staff Mr. Guruswamy trained can now treat their patients quickly and avoid the three to four week wait for culture results. 

Mr. Guruswamy is also involved in ASM’s Minority Mentoring Program so he can offer younger scientists the kind of assistance he says he got from other ASM members back at the beginning of his own career, when he arrive in the United States with less than $50 in his pocket. 

In this interview, I asked Mr. Guruswamy about his work at the state lab in Virginia, about tuberculosis in this country, and about why he saw more unusual clinical cases during his time working at the Mayo Clinic in Minnesota than he has during any other phase of his career.

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MTS31 - Frances Arnold - Engineering Microbes

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jul 15, 2009

Dr. Frances Arnold is a professor of Chemical Engineering and Biochemistry at the California Institute of Technology (most of us know it as Caltech).  Dr. Arnold’s research focuses on evolutionary design of biological systems, an approach she is currently applying to engineer cellulases and cellulolytic enzymes for manufacturing biofuels.

 This country’s energy security can look pretty bleak when you think about it: the need to address global warming, strife in oil-rich nations, and depletion of fossil fuels combine to paint an uncertain future, and although ethanol has a lot of friends in Iowa and D.C., ethanol isn’t going to end our energy woes.  In the future, our energy supply will probably be cobbled together from a number of different fuels and sources.  

Dr. Arnold is interested in engineering microbes that can grant us a biofuel that packs more of a caloric punch than ethanol.  She likes isobutanol, which can be converted into a fuel that’s more like the hydrocarbons we currently put into our fuel tanks.  To develop proteins that make the comounds she wants the way she wants, Arnold and her team take a gene that needs tweaking to do the job, introduce directed mutations into it, and select the mutant proteins that do the job best.  

In this interview, I talked with Dr. Arnold about how she got into alternative energy during the Carter administration (and got out again during the Reagan administration), what she sees in the P450 enzyme, and how she explains her work to people outside her field.

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MTS30 - Stanley Plotkin - The Past, Present, and Future of Vaccines

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jul 01, 2009

Stanley Plotkin is Professor Emeritus at the Wistar Institute and the University of Pennsylvania, Philadelphia.  A renowned vaccinologist, Dr. Plotkin is, perhaps, best known for developing a highly successful vaccine for rubella back in 1968.  We are still using the same vaccine 40 years later.  Dr. Plotkin has been honored with the inaugural Maurice Hilleman / Merck Award for his lifetime of dedication to vaccinology. 

For most people, rubella amounts to a bad rash and a crummy week, but for a fetus, the risks from infection are extremely serious.  The rubella virus inhibits tissue growth in infected fetuses, often resulting in profound birth defects collectively referred to as congenital rubella syndrome. 

Dr. Plotkin developed the rubella vaccine in the wake of a rubella pandemic in 1964, during which he estimates that about 1 in 100 women in his home city of Philadelphia came down with rubella.  Nationwide, thousands of babies were born with congenital rubella syndrome in the wake of the outbreak.  Thanks to the vaccine developed by Dr. Plotkin, rubella has essentially been eradicated in the U.S. and most other developed countries.  In many parts of the developing world, efforts are underway to piggy back the rubella vaccine with the measles vaccine to eradicate both of these diseases everywhere else. 

In this interview, I talked with Dr. Plotkin about the backlash against vaccines for their perceived safety risks, how he would change vaccine policy, and about the rewards of a career in vaccine development.

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MTS29 - Christine Biron - The Innate Immune System

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Jun 18, 2009

Christine Biron is the chair of the Department of Molecular Microbiology and Immunology at Brown University in Providence, and she focuses her research program on the mechanisms of the innate immune system – the body’s system of non-specific munitions for fighting off pathogens.  Dr. Biron is also a newly elected fellow of the American Academy of Microbiology.

When a pathogen gets on or in your body, your innate immune system is on the front lines, working against the pathogen is a non-specific manner.  In research, the innate immune system got short shrift for a long time, and only in the last 10 or 20 years has the field picked up momentum.  Dr. Biron says back when she was in graduate school “the innate immune system wasn’t thought to be very cool”, but she says the field is fast-moving today, in part because of some major discoveries involving Type-1 interferons, natural killer cells, and an increased appreciation of a wider range of antigen processing cells that link the innate and adaptive immune responses.

In this interview, I talked with Dr. Biron about our increasing awareness of the innate immune system, why it’s important to bring microbiologists and immunologists together under one big tent, and why it’s best that a battle between a virus and a host ends not in victory for one and defeat for the other, but in d?tente.

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MTS28 - Joseph DeRisi - New Tech Approaches to Infectious Disease

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Tue, Jun 02, 2009

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.

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MTS27 - Melanie Cushion - Pneumocystis carinii

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, May 14, 2009

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.

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MTS26 - Ian Orme - Tuberculosis

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, May 07, 2009

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-Gu?rin).

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.

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MTS25 - Parisa Ariya - Bioaerosols | The Living Atmosphere

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Apr 23, 2009

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.

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MTS24 - Jeff Bender - MRSA in Animals

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Apr 17, 2009

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.

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MTS23 - Jo Handelsman - The Science of Bug Guts

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Apr 10, 2009

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.

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MTS22 - David Knipe - Herpes Simplex Virus 2 (HSV-2)

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Tue, Mar 31, 2009

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.

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MTS21 - Andrew Knoll - Ancient Life and Evolution

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Tue, Mar 17, 2009

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.

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MTS20 - Roberto Kolter - Bacillus Subtilis and Bacteria as Multicellular Organisms

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Mar 12, 2009

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.

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MTS19 - Ellen Jo Baron - The Challenges and Rewards of Working in the Developing World

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Mar 05, 2009

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.

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MTS18 - Elizabeth Edwards - Cleaning Up Solvents in Groundwater

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Feb 25, 2009

Elizabeth Edwards knows that nothing is simple or easy when it comes to cleaning up toxic waste, but Edwards, a professor of Chemical Engineering and Applied Chemistry at the University of Toronto, is looking for ways to harness microbes to do our dirty work for us.  Dr. Edward’s research focuses on the biodegradation of chlorinated solvents in the environment – the means by which microbes can actually make a living by eating our noxious waste.

Chlorinated solvents like trichloroethylene (TCE), perchloroethylene (PCE), and others, have a sordid history in the environment.  They have long been used as degreasers and dry cleaning fluid, but before there were regulations about how to handle waste, manufacturers and dry cleaners dumped old, dirty solvents in evaporation ponds or out the back door of the facility.  Some of the fluid dumped this way evaporated, but since chlorinated solvents are both dense and recalcitrant, much of the liquid seeped straight down to the groundwater.  And stayed there.  Among other projects, Dr. Edwards is looking at the ability of mixed cultures of bacteria to break down these solvents in a step-wise process, with the expectation that we’ll eventually be able to treat the contamination at some sites with injections of microbes.

In this interview, Dr. Merry Buckley talks with Dr. Edwards about why chlorinated solvents are such a difficult environmental problem, how working in environmental consulting for a time helped her realize where she wanted to focus her research, and why we might have to make some tough decisions when it comes to cleaning up the hundreds (thousands?) of solvent-contaminated sites in North America.

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MTS17 - Stuart Levy, MD - Antibiotic Resistance and Biosecurity

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Feb 12, 2009

If you or someone you care about has ever had an antibiotic resistant infection, you know how dire that situation can be.  Stuart Levy, a professor of microbiology at Tufts University in Boston, has centered his research around the theme of antibiotic resistance and he says there are few antibiotics in the pipeline for use on that inevitable day when our current infection-fighters are finally overcome.  Dr. Levy is delivering the keynote address at ASM’s Biodefense and Emerging Diseases Research Meeting in Baltimore in February.

Antibiotic resistance may not be making big headlines these days, but that’s not because the threat is any less serious than before.  Levy says he first became interested in antibiotics as a child, when he watched a course of antibiotics heal his twin brother, who suffered from an infection.  Later, as a researcher at the Pasteur Institute in Paris, France, he learned that bacteria can swap around the ability to resist antibiotics, and that failing to manage a small problem with resistance can have some serious consequences down the line.

In this interview, I talked with Dr. Levy about his talk at the biodefense meeting, what antibiotic resistance has to do with biosecurity, and about why you should leave those bottles of antimicrobial soap on the shelves at the store.

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MTS16 - Paul Keim, Ph.D. - The Science Behind the 2001 Anthrax Letter Attacks

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Mon, Feb 02, 2009

Dr. Paul Keim is a professor of biological sciences at Northern Arizona University, in Flagstaff, where his research program focuses on microbial forensics and the genomic analysis of pathogenic bacteria.  As an expert in Bacillus anthracis, the bacterium responsible for anthrax, Dr. Keim participated in the FBI’s investigation into the anthrax letter attacks back in 2001.

Microbial forensics is a field that developed in response to the twin threats of biological warfare and biological terrorism.  (What’s the difference between biological warfare and biological terrorism?  Both have the potential to reach beyond the site of the attack and both are a menace to innocent, unarmed citizens.  To me, there’s a fine line here.  But I digress.)

Dr. Keim’s interest in microbial forensics arose out of his postdoctoral work at the University of Utah.  After this training in phage recombination and genomics, Dr. Keim applied what he had learned about bacterial genetics in a collaboration with scientists working on resolving and identifying the various strains of B. anthracis.  Fast forward to this past summer, when the F.B.I. revealed that Dr. Keim used his expertise on B. anthracis to help in the investigation that concluded a researcher at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) perpetrated the anthrax attacks.  Dr. Keim, along with several other scientists who helped in the F.B.I.’s


In this podcast, I talked with Dr. Keim about his work with the F.B.I., whether the payoffs of bioterrorism research are worth the costs, and about how the plague (yes, the Black Death) made its way to North American shores and continues to sicken about a dozen people every year.

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MTS15 - Kathryn Boor - The Science of Foodborne Pathogens

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jan 21, 2009

Dr. Kathryn Boor is a professor and chair in the Food Science department at Cornell University, where she’s director of the Food Safety Laboratory - a biosecurity level 2 laboratory that facilitates research on foodborne pathogens.  Her particular research interests lie in the “how” and “why” of pathogens and spoilage microbes in food.  Boor is also the director of the Milk Quality Improvement Program – a program funded by New York state to monitor and make recommendations to improve the quality of milk in the state.

When I think about the complicated way dairy products come to be on the shelf in my grocery store – farmers use machinery to extract milk from an animal that lives in a barn or a field; the milk is piped through long tubes to a tank on a truck that conveys the product to a plant that processes and divvies it up; the bottles and packages are put on another truck and carted to the store – it seems like a wonder dairy is ever safe to eat.  But dairy is safe: CDC data indicate that less than 1% of foodborne illness outbreaks in the U.S. involve dairy products1 2 .

Dr. Boor’s primary interest lies in Listeria monocytogenes, one of the few pathogens that is a problem in dairy, and most people who’ve heard of it associate it with unpasteurized soft cheese or cold cuts.  Listeriosis is not as common or familiar as some other foodborne illnesses, but it is more often fatal than salmonellosis or botulism, and in a pregnant woman even a mild case can be deadly for her fetus.  Dr. Boor’s research focuses on how this so-called “simple” organism is able to persist in some foods and overcome the stress of refrigeration and stomach acid to not only survive, but to make us really sick.

In this interview, I asked Dr. Boor about how she came to this particular niche in science, whether pasteurization is any better than keeping milk from getting contaminated in the first place, and what her trained eye for food safety looks out for when she’s buying food.

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MTS14 - Moselio Schaechter - Successful Science Blogging and Hunting Mushrooms

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Jan 07, 2009

Moselio Schaechter – known as Elio to his friends – is Distinguished Professor of Molecular Biology and Microbiology, Emeritus, at the Tufts University School of Medicine, and he’s currently an adjunct professor at San Diego State University and at the University of California at San Diego. Dr. Schaechter has had a long career in bacteriology and has authored or co-authored a number of text books, and is a former president of the American Society for Microbiology. He lives in sunny San Diego now, where he lectures, attends meetings, and writes his blog, “Small Things Considered”.

If you want an example of the ways the internet has changed public discourse, look to the blogs - you’re reading one now, after all, and how many blogs did you read 10 years ago? Blogs give authors a bullhorn free from profit-driven publishers, provide people with ideas, and even build communities through reader discourse. To be sure, not every blog is interesting or even readable, but there are many bloggers out there working hard and stimulating some profound discussions.

Those of us interested in the life microscopic are lucky to have Dr. Schaechter, who muses on the topics of interest to him and acts as host to other eminent scientists who write guest essays. With Small Things Considered, his goal is to express his own interest in various subjects while encouraging interest in others and kindling conversation and debate.

In my interview with Dr. Schaechter, we talk about what he gets out of being a blogger, what makes for a successful blog, and about how mushroom hunting in xeric Southern California usually involves a lot of hunting and few mushrooms.

Blogs and Websites mentioned in this episode include:

The Loom by Carl Zimmer

Esos Pequenos Bichitos

Le blog des bacteries et de l’evolution

Aetiology by Tara C. Smith

Microbiology Bytes

The Registry of Mushrooms in Works of Art

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MTS13 - Video Supplement - Proteopedia Video Guide

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Dec 31, 2008

This is a video supplement to the audio podcast of Meet the Scientist episode 13 in which I interview Joel Sussman, Ph.D., a professor of structural biology at the Weizmann Institute of Science in Israel. The video shows Sussman's Proteopedia.org in action. It is narrated by Eran Hodis, the graduate student, who, together with Professors Jaime Prilusky and Joel L. Sussman developed Proteopedia at the Weizmann Institute of Science.

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MTS13 - Joel Sussman - Proteopedia.org and Intrinsically Unstructured Proteins

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Wed, Dec 31, 2008

Joel Sussman, Ph.D. is a professor of structural biology at the Weizmann Institute of Science in Israel. In his research, Dr. Sussman is interested in elucidating the structures and functions of proteins, particularly those involved in the nervous system. He is also the lead scientist behind Proteopedia – a new online protein structure encyclopedia.

Scientific endeavors have historically been a one-way street: an investigator or lab makes a discovery, then delivers the good news to the rest of the community via publication. Nowadays, computers and the internet are enabling easier and more seamless means of collaboration and communication. Proteopedia, with which Dr. Sussman is greatly involved, automatically gathers and compiles information from multiple curated sources of information, but its more revolutionary side is the wiki tool, which enables registered users to contribute information themselves.

In this interview with Dr. Sussman, I talked with him about his work with acetylcholinesterase and “intrinsically unstructured proteins” and about Proteopedia – how it works and about the possibility of misinformation making its way onto the site.

The video extra shows Proteopedia in action. It is narrated by Eran Hodis, the graduate student, who, together with Professors Jaime Prilusky & Joel L. Sussman developed Proteopedia at the Weizmann Institute of Science.

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MTS12 - Nancy Keller - Aspergillus and the Fungal Toxin Problem

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Tue, Dec 23, 2008

Nancy Keller is a Professor of Bacteriology and Medical Microbiology and Immunology at the University of Wisconsin-Madison. A mycologist, Dr. Keller works with a genus of fungi called Aspergillus – many of which are potent plant and human pathogens that produce deadly mycotoxins. Her research focuses on finding those aspects of Aspergillus species that make them effective as pathogens and toxin factories.

Tiny fungi cause big problems for agriculture and human health, and the U.S. alone spends millions of dollars every year to fight the fungi that attack crops. Aspergillus fungi, in particular, cause a problem for crop plants themselves, but the bigger concern is the mycotoxins they produce: aflatoxin is one of the most potent naturally-occurring toxins ever discovered. What’s more, aflatoxin and other Aspergillus toxins are carcinogenic. The bottom line? Exposure to large amounts of these fungal toxins can kill you quickly, and exposure to small amounts can kill you slowly.

On this episode, I talk with Dr. Keller about her work with Aspergillus, why we don’t even know how big the fungal toxin problem is, how reproduction and toxin-making are linked in these fungi, and how we may eventually use viruses as weapons against pathogenic fungi.

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MTS11 - Daniel Lew - The Yeast Cell Cycle

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Mon, Dec 08, 2008

Daniel Lew is a professor of Pharmacology and Cancer Biology and of Genetics at the Duke University Medical Center in Durham, North Carolina.  His research program focuses on cell cycle control in yeast, and how the cell cycle interacts with cell polarity.

Yeast cells may look simple, but inside every little single-cell package lurks an intricate creature that senses and responds cunningly to its surroundings.  Dr. Lew has uncovered many of the secrets of the tiny yeast, and since yeast bear a striking resemblance to human cells, some of these facts could help us eventually conquer our own problems with the cell cycle, including cancer – a kind of cell division gone wild.

In this interview, I talk with Dr. Lew about how a yeast cell knows when to say “when” during budding, why he studies yeast at a medical school, and where his hard-to-discern accent really comes from (hint: it’s not a North Carolina accent).

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MTS10 - Anthony Maurelli - Black Holes and Antivirulence Genes

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Tue, Nov 25, 2008

Tony Maurelli is a professor of microbiology and immunology in the F. Edward H?bert School of Medicine at the Uniformed Services University of the Health Sciences in Bethesda, Maryland.  Dr. Maurelli’s major research interest lies in the genetics of bacterial pathogenesis – the genetic nuts and bolts of how bacteria infect humans and make us sick.

Dr. Maurelli’s work has uncovered “antivirulence genes” in Shigella flexneri, a major cause of dysentery and food borne illness.  This is an interesting concept: antivirulence genes undermine pathogenicity, so they must be broken or dropped from the genome for a bacterium to take good advantage of a host and cause disease.  These genes are a hindrance, so to become an effective pathogen, Shigella must stop using them.

In this interview, I talked with Dr. Maurelli about antivirulence genes, about whether the naming system for bacteria should be fixed, and about his favorite bacteria.

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MTS9 - Stanley Falkow - 21st Century Microbe Hunter

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Nov 21, 2008

Stanley Falkow is a professor of Microbiology & Immunology at the Stanford School of Medicine. His research interests lie in bacterial pathogenesis – how bacteria cause infection and disease – and over the course of his career he has contributed fundamental discoveries to the field. Falkow received the Lasker prize this year for special achievement in medical science, and the Lasker Foundation calls him “one of the great microbe hunters of all time”.

Molecular techniques (methods of analysis that rely on bacterial DNA) are now widely used for infectious disease diagnosis, thanks in large part to Falkow, who was among the first to apply an understanding of genes and virulence determinants to analyzing patient samples. He has published extensively in areas ranging from antibiotic resistance to food borne illness to microarrays. It is really difficult to compose interview questions for a scientist whose career has been as far-reaching and profoundly significant as Stan Falkow’s. Luckily for me, Dr. Falkow is a gracious conversationalist.

In this interview, I talked with Dr. Falkow about his prescient concerns about the dangers of using antibiotics as growth promoters in livestock, why Salmonella is so good at making you sick, and why students who are interested in science should follow their passion.

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MTS8 - Rachel Whitaker - The Evolution of Sulfolobus

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Nov 14, 2008

Rachel Whitaker is an assistant professor of microbiology at the University of Illinois at Urbana-Champaign, where she has developed a research program focused on the evolutionary ecology of microorganisms. Much of Dr. Whitaker’s work centers around a hyperthermophile found in geothermal springs: the archaeon Sulfolobus islandicus.

Evolution is not just history – it’s still in action today, molding humans, plants, animals and, of course, microbes, in ways we still don’t completely understand. One of Whitaker’s focus areas is archaea, a group of single-celled microbes that are found in some of the harshest environments on earth. By looking at how one variety of archaea, Sulfolobus, varies from place to place, Whitaker hopes to find whether Sulfolobus is adapting new characteristics to suit its habitats, and whether this kind of adaptation can help us explain why there are so many different kinds of microbes in the world.

In this interview, I asked Dr. Whitaker about the hot springs where she studies Sulfolobus, whether it’s hard to communicate with ecologists who work with bigger organisms, and about new discoveries she’s made related to an immune system in archaea.

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MTS7 - Anthony Fauci - Managing Infectious Disease on a Global Scale

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Tue, Nov 11, 2008

Dr. Anthony Fauci is the director of NIAID – the National Institutes for Allergy and Infectious Disease – where he is also Chief of the Laboratory of Immunoregulation. Dr. Fauci’s research interests lie primarily in the molecular mechanisms of HIV and AIDS, and he has published extensively on the interactions of HIV with the immune system. He’ll be speaking at the opening session of ICAAC – the Interscience Conference on Antimicrobial Agents and Chemotherapy – on October 25 in Washington DC, where he’ll describe some of the remaining challenges in the fight against HIV, tuberculosis, and antibiotic resistant microbes.

Dr. Fauci is not only a researcher, he is also an important player in science policy in the U.S. He was a primary architect of PEPFAR, the President’s Emergency Plan for AIDS Relief, a program that received reauthorization and has a budget of $48 billion for HIV/AIDS, tuberculosis, and malaria around the world. In honor of his efforts to improve our understanding and treatment of HIV and AIDS, Dr. Fauci was recently awarded the Presidential Medal of Freedom, the nation’s highest civil award.

In this interview, I talked with Dr. Fauci about progress in managing infectious disease on a global scale, why it’s the “devil you don’t know” that is still the scariest infectious disease of all, and about the roles of abstinence education and condom awareness in PEPFAR.

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MTS6 Bruce Rittmann - Microbes, Waste and Renewable Energy

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Oct 09, 2008

Bruce Rittmann, the Director of the Center for Environmental Biotechnology at the Biodesign Institute of Arizona State, focuses his efforts on reclaiming contaminated water and producing renewable energy using microbes.

He was elected to the National Academy of Engineering in 2004 and credited with pioneering development of biofilm fundamentals and contributing to their widespread use in the bioremediation of contaminated ecosystems. His research combines many disciplines of science, including engineering, microbiology, biochemistry, geochemistry and microbial ecology. Formerly with Northwestern University, Rittmann is also a leader in the development of the Membrane Biofilm Reactor, an approach that uses bacteria to destroy pollutants in water. The Membrane Biofilm Reactor is especially effective for removing perchlorate from drinking water, and it is being launched commercially.

In this podcast, I talk with Dr. Rittmann about the biofilm reactor process, the electricity hiding in our wastewater, and how we may some day grow fuel on the roofs of buildings.

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MTS5 Brett Finlay - E.coli and the Human Gut

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Oct 02, 2008

Brett Finlay is a professor in the Michael Smith Laboratories, and the Departments of Biochemistry and Molecular Biology, and Microbiology and Immunology at the University of British Columbia.

His research program focuses on E. coli, how it interacts with the cells of the human gut, and mouse models of E. coli-like infections.  Dr. Finlay will speak at the conference on Beneficial Microbes in San Diego this October, where he’ll describe the results of some of his latest research, which examines how E. coli infections effect the microbes that live in our guts.

Sadly, outbreaks of Escherichia coli infections in this country are common – just this summer a huge E. coli outbreak in Oklahoma sickened nearly 300 people and sent 67 of them to the hospital.  Clearly, in an outbreak, not everyone is effected equally.  When lots of people are exposed to E. coli, why do some of those people walk away unharmed while others wind up in the I.C.U.?  Dr. Finlay would say part of the answer, at least, probably lies in which microbes live in our intestine.

In this podcast, I talked with Dr. Finlay about why we have so many different kinds of microbes in our guts, what happens to them when E. coli strikes, and why we have a long way to go before probiotics offer help – and not just hope.

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MTS4 David Relman - The Human Microbiome

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Thu, Sep 25, 2008

David Relman is a Professor of Medicine and of Microbiology & Immunology at Stanford University, and his research program focuses on the human microbiome – the microbial communities of bacteria, viruses, and other organisms that thrive on and in the human body. He’ll be speaking at ASM’s conference on Beneficial Microbes in San Diego this October, where he’ll talk about our personal microbial ecosystems, how far we’ve come in research and how far we have to go.

Since Louis Pasteur first deduced that microbes are to blame for infectious disease, doctors and scientists alike have mostly seen infection as warfare between a pathogen and the human body. Dr. Relman sees things a little differently. To him, the complex communities of microbes that line our skin, mouths, intestines, and other orifices (ahem) are also involved in this battle, interacting with pathogens and with our bodies, and these interactions help determine how a fracas plays out.

In this interview, I asked Dr. Relman about our personal ecosystems of microbes, whether we’ll ever be able to understand and predict what these communities do, and about the sometimes distressing effects of oral antibiotics on our guts. We also talked about whether being MTV’s Rock Doctor back in the 1990’s had an impact on his other professional pursuits.

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MTS3 Ute Hentschel - Symbiotic Sea Sponges

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Fri, Sep 19, 2008

Ute Hentschel is a professor of chemical ecology at the University of W?rzburg in Germany. Her research focuses on characterizing the microbial communities associated with marine sponges, the diversity of these symbionts and their activities.

On this episode, I talk with Ute Hentschel about her research on the microbes that live on and in sea sponges – those squishy, colorful residents of coral reefs.

Dr. Hentschel describes some of the utterly unique microbes that are only found in sponges, what those microbes get from living in a sponge hotel, and why it’s nice to have a study site in the Bahamas.

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MTS2 - Seth Darst - RNA polymerase

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Tue, Sep 09, 2008

Seth Darst is a professor of Molecular Biophysics at the Rockefeller University in New York city, where his research centers on RNA polymerase, the enzyme at the heart of a cell’s ability to make protein from a set of DNA instructions.

In this interview, I talk with Dr. Darst about how he got his start in research, whether computers will eventually be able to predict complex protein structures, and why eager young scientists shouldn’t miss their chance at postdoctoral training.

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MTS1 Ralph Tanner - The Future of Biofuels

ccondayan@asmusa.org (Carl Zimmer)Author: Carl Zimmer
Mon, Aug 18, 2008

Ralph Tanner, a professor of microbiology at the University of Oklahoma, focuses his research on anaerobes in the environment and putting those bacteria to use in industry.

He develops useful microbial catalysts for biofuel production from sustainable crops and has extended our knowledge of microbial diversity by isolating a number of new genera and species with novel physiologies. He helped define the phylogeny of bacteria.

In this podcast, I talk with Dr. Tanner about his work producing biofuels from burnt plant material, the future of biofuels in the U.S., whether bacterial systematics might be forced to change in light of new research on recombination, and about his approach to teaching microbiology.

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