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Matters Microbial #66: Digesting the Science of Fermented Foods November 20, 2024
Today, Dr. Ben Wolfe, Associate Professor of Biology at Tufts University, joins the #QualityQuorum to discuss how he and his collaborators study novel food fermentations, helping the public understand more about the gut microbiome, and outreach projects involving microbially-associated food.
Host: Mark O. Martin
Guest: Benjamin Wolfe
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Links for this episode An overview for beginning Micronauts on microbial fermentation. A more advanced overview of microbial fermentation. A book and website that I highly recommend by Sandor Katz on the subject, including many recipes and background information. The bacterially derived volatile chemical geosmin. An article describing the relationship between geosmin and springtails. An article about leaf cutter ants and how they farm fungi! I hope to do an entire podcast on this topic soon. An article of Dr. Wolfe and colleague’s work showing a relationship between fungal antibiotics and cheese microbiome development. Dr. Rob Dunn’s “Belly Button Microbiome” project, a community science effort. An overview of the community science effort to explore sourdough bread microbiology. An overview of cheese microbiology. A description of cheesemaking and cheese caves. A cheesemaker with which Dr. Wolfe has worked. A link to a remarkable article by Dr. Wolfe’s research group that we discussed in this episode: “Novel Fermentations Integrate Traditional Practic and Rational Design of Fermented-Food Microbiomes.” A video of a presentation by Dr. Wolfe on cheese microbiology. Dr. Wolfe’s faculty website at Tufts University. A website by Dr. Wolfe and coworkers promoting microbial literacy via understanding the positive relationship between food and microbes. The website of Dr. Wolfe’s research group.Intro music is by Reber Clark
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Today, Dr. Alex Bisson, Assistant Professor of Biology at Brandeis University, joins the #QualityQuorum to discuss how he and his collaborators use a variety of tools to study the mechanobiology of archaea (such as how some respond to being “squished”), and how those studies can shed light on the evolution of complex eukaryotes like humans.
Host: Mark O. Martin
Guest: Alex Bisson
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Links for this episode An overview of one of the archaea used by Dr. Bisson’s research team, Haloferax volcanii. Here is an article from New Scientist about Dr. Bisson’s research. A journal article from Nature Communications describing work done by the Bisson laboratory. The preprint from Dr. Bisson’s research team discussed in this podcast. Here is a video of a seminar by Dr. Bisson. Dr. Bisson’s faculty website. Dr. Bisson’s very interesting research team website.Intro music is by Reber Clark
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Today, Dr. Patrick Schloss, Professor in the Department of Microbiology and Immunology in the School of Medicine at the University of Michigan, joins the #QualityQuorum to discuss how the human microbiome is studied, possible pitfalls in such data analysis, and what tools he and his coworkers have developed to lead toward repeatable, hypothesis-driven science.
Host: Mark O. Martin
Guest: Patrick Schloss
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Links for this episode An overview of how the gut microbiome is analyzed. One of the articles discussed by Dr. Schloss exploring reproducibility in microbiome studies: “Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research.” Another article discussed by Dr. Schloss, regarding the link between the microbiome and obesity: “Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome.” An article from Dr. Schloss’ research team that explores a link between the human microbiome and a type of colorectal cancer. A link to the MOTHUR project, used to analyze microbiome data. A link to a video by Dr. Schloss: “Understanding Disease Through the Lens of the Microbiome.” Dr. Schloss’ YouTube channel about data analysis. Dr. Schloss’ research group website. Dr. Schloss’ faculty website.Intro music is by Reber Clark
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Matters Microbial #63: A Symphony of Cyanobacteria October 30, 2024
Today, Dr. Nathan Algren, Associate Professor of Biology at Clark University, joins the #QualityQuorum to discuss the centrality of cyanobacteria to our biosphere, the viruses that prey upon them, and his interests in outreach and science-oriented art.
Host: Mark O. Martin
Guest: Nathan Ahlgren
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Links for this episode An overview of the cyanobacteria. An overview of Prochlorococcus. An overview of marine bacteriophages. The Great Oxidation Event Cyanobacteria are thought to have radically changed our planet 2.5-3.5 billion years ago by producing oxygen through photosynthesis. In essence, they and other microbes are the original terraformers. The Purple Earth Hypothesis Photosynthesis as we know it, using chlorophyll, may have evolved after another way of doing photosynthesis, with retinal that looks purple. This means that our planets and other ‘younger’ planets may look or have looked purple rather than green. Self-assembly of viral capsids, as modeled by 3D-printed parts (Art Olson) TED talk from Penny Chisholm on Prochlorococcus Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron Study showing how different populations of Synechococcus occupy different niches and regions of the oceans according to their adaptations to temperature and nutrients. Long-term stability and Red Queen-like strain dynamics in marine viruses Study showing turnover of strains within relatively stable phage populations. Viral treadmills in the ocean—running to stand still Companion ‘behind the paper’ article. Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics Paper showing cyanophage ‘species’ have different time patterns in the oceans. Rapid diversification of coevolving marine Synechococcus and a virus
Study showing stable co-existence and co-evolution of a single Synechococcus host and phage over time. The emergence of resistance hosts and phage that overcome them demonstrate the principles of the Red Queen hypothesis and phage-host ‘arms race’. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus Figure from this paper is in the presentation. Shows modeled distributions of Pro and Syn across the globe. They also use this to estimate a ~25% contribution of Pro and Syn to global net primary productivity in the oceans. Link to 3D prints that Dr. Ahlgren made an are available on NIH page Some resources on how to 3D protein structures: I like this guide on the practical guide of how to do actually to do it (going from PDB to print files): A link to another resource for 3D printing of protein structures. Dr. Ahlgren’s faculty website. Dr. Ahlgren’s laboratory website with many fascinating links.Intro music is by Reber Clark
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Matters Microbial #62: Should I Stay, or Should I Go—How Bacteriophage are Released from Host Cells October 23, 2024
Today, Dr. Jolene Ramsey, of the Biology Department of Texas A&M University and Affiliate of the Center for Phage Technology, joins the #QualityQuorum to discuss how bacteriophages release themselves from host cells, her efforts to teach students to work with the primary literature, and her own path to the microbial sciences.
Host: Mark O. Martin
Guest: Jolene Ramsey
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Links for this episode A truly wonderful reminder video about bacteriophages. A link with a 3D printer design of capsid model pieces (personally, I am really interested in making one of these!). A video demonstrating how the capsid model pieces self assemble—something like real viruses can? An essential book about bacteriophage authored by my late friend Merry Youle. A fine book describing how bacteriophages can be used to fight bacterial diseases. This “first person” book by #MattersMicrobial podcast guest Steffanie Strathdee about how she was able to use bacteriophages to save her husband’s life is a must read. A link to the Citizen’s Phage Library. A link to the truly fabulous (yes, I am jealous I am not part of this program) CURE program SEA-PHAGES and SEA-GENES for undergraduate students. A remarkable illustration of T4 bacteriophage bursting from host cells by the scientist-artist David Goodsell. The organization that designed Dr. Ramsey’s laboratory logo. A link to the Clinical Genome Curation for Human Genes. A link to the CACAO website for biocuration competition. A recent Ramsey lab mini-review on phage classification. A link to the Center for Phage Technology. The Ramsey lab Instagram page. The Ramsey lab YouTube channel. Dr. Ramsey’s laboratory website. Dr. Ramsey’s faculty website.Intro music is by Reber Clark
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Matters Microbial #61: All In Due Time–How Bacteria Wake from Dormancy October 17, 2024
Today, Dr. Paul Carini, of the Environmental Science department of the University of Arizona, joins the #QualityQuorum to discuss how soil bacteria can become dormant, “wake up,” and why that is more relevant than you might suppose.
Host: Mark O. Martin
Guest: Paul Carini
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Links for this episode A lovely essay about the “Cultivation Conundrum”: why so many microbes in nature cannot be grown in the laboratory. The “uncultivated majority” is often called “microbial dark matter,” described here. An essay about the scale of microbiology with some fascinating facts. Arizona Culture Collection project by Dr. Carini and colleagues. Dilution to extinction technique An overview of sporulation, including some fascinating variations. A description of Arthrobacter A description of Bradyrhizobium An essay explaining PCA plots An essay about intrinsically disordered proteins A very nice video about working in Dr. Carini’s lab. HIGHLY RECOMMENDED. Dr. Carini’s faculty website. Dr. Carini’s fascinating laboratory website. Dr. Carini’s Substack page, where he explores many microbiological ideas.Intro music is by Reber Clark
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Matters Microbial #60: Influenza, Epidemics, Pandemics, and Fortunate Mistakes October 9, 2024
Today, Dr. Adam Lauring of the University of Michigan joins the #QualityQuorum to discuss the job of a physician-scientist, RNA viruses, the tricks that influenza uses to create epidemics and pandemics, and the science behind flu vaccines.
Host: Mark O. Martin
Guest: Adam Lauring
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Links for this episode A description of the MD/PhD path in science. An introduction to RNA viruses. An article describing different types of RNA viruses. The history of influenza. An overview of the influenza virus. An essay on the shift/drift issue in influenza. A more formal review of the shift/drift issue in influenza. A video about the evolution of RNA viruses. An essay about influenza virus evolution describing some of Dr. Lauring’s work. Dr. Lauring and his colleague’s fascinating research lab page. Dr. Lauring’s faculty website.Intro music is by Reber Clark
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Matters Microbial #59: Some (Microbes) Like It Hot—Discussions with the Thermal Biology Institute October 3, 2024
Today is an unusual episode of the podcast. I am visiting four microbiologists in the Thermal Biology Institute at Montana State University of Bozeman, Montana. They discuss their work exploring the unusual microbes and environments to be found in Yellowstone National Park, ranging from the history of the park to opportunities for undergraduate students, as well as up-to-the-minute research done on the microbial denizens of this microbiological landmark.
Host: Mark O. Martin
Guests (in order of appearance:): Brent Peyton, Dana Skorupa, Zackary Jay, Anthony Kohtzy
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Links for this episode A history and overview of Yellowstone National Park. An overview of microbiology in Yellowstone National Park. The story of Yellowstone National Park and PCR. Website for the Thermal Biology Institute. A prior podcast of #MattersMicrobial involving Dr. Roland Hatzenpichler and the research done by several of today’s guests. Dr. Peyton’s faculty website. Dr. Peyton’s laboratory website. Dr. Skorupa’s faculty website. A great article on the adventurous REU (Research Experience for Undergraduates) that Dr. Skorupa supervises. Dr. Jay’s faculty website. A journal article describing some of Dr. Jay’s (and Dr. Kohtz’) work. A page including Dr. Kohtz An article describing some of Dr. Kohtz’ (and Dr. Jay’s) work.Intro music is by Reber Clark
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Today, Dr. Cynthia Silveira of the Department of Biology at Miami University joins the #QualityQuorum to discuss her research team’s efforts to explore how bacterial viruses interact with their host cells from coral reefs to other planets! In addition, Dr. Silveira will discuss her microbiological path and a course she teaches on virology.
Host: Mark O. Martin
Guest: Cynthia Silveira
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Links for this episode A video about marine bacteriophages and the role they play in ecological systems. A fine article about the role that bacteriophages can have in marine environments. An essay suggested that marine viruses may influence global climate. A link to the wonderful book, “Coral Reefs in a Microbial Sea.” Forest Rohwer’s laboratory website. The role of a retrovirus in the development of the mammalian placenta. A bacterial role in snow making, using the commercial product “Snomax.” A “faculty spotlight” essay on Dr. Silveiro. Dr. Silveiro’s laboratory website. Dr. Silveiro’s faculty website.Intro music is by Reber Clark
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Matters Microbial #57: Pitting Metabolic Inhibitors Against Viruses September 18, 2024
Today, Dr. Tracie Delgado of the Biology Department at Seattle Pacific University joins the #QualityQuorum to discuss her undergraduate research team’s explorations of how some herpesviruses can cause cancer . . . and how to use the host cell’s metabolism to fight those viruses!
Host: Mark O. Martin
Guest: Tracie Delgado
Download MM#57 (39 MB mp3, 65 min)
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Links for this episode An overview of the herpesviruses as a group. A description of gammaherpesvirus, the type of herpesvirus with which Dr. Delagado and colleagues work. The relationship between some herpesviruses and cancer. The mysterious Warburg Effect, discussed by Dr. Delgado today. A wonderful TED talk by Dr. Delgado. A talk Dr. Delgado gave at a 2017 March for Science Event, arguing for more and better representation in STEM. An article about Dr. Delgado’s journey to science. Dr, Delgado’s research team’s website with links to research articles that were discussed. Dr. Delgado’s faculty website.Intro music is by Reber Clark
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Matters Microbial #56: Marine Microbial Echoes of Evolution September 11, 2024
Today, Dr. Carolina Martinez Gutierrez of the Department of Earth Science at the University of California Santa Barbara joins the #QualityQuorum to discuss her research team’s efforts to unravel how ancient microbes thrived in the early oceans of Earth’s history . . . and to sing the praises of marine microbiology!
Host: Mark O. Martin
Guest: Carolina Martinez Gutierrez
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Links for this episode An overview of the microbiome of the ocean and geochemistry. A description of likely conditions on Ancient Earth. An essay about the Great Oxidation Event—the event that changed our entire planet. An article by Dr. Martinez Gutierrez and colleagues discussing how phylogenomics can help dissect microbial evolution without fossils. An overview of Prochlorococcus, one of the microbes Dr. Martinez Gutierrez discussed. A wonderful video about Prochlorococcus and a remarkable scientist. An overview of Pelagibacteri ubique (SAR11), one of the microbes Dr. Martinez Gutierrez discussed.
An article about the work of Dr. Martinez Gutierrez and her research interests while a postdoctoral scholar The departmental website for Dr. Martinez Gutierrez The laboratory website for Dr. Martinez Gutierrez’s research group.Intro music is by Reber Clark
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Today, the award winning and affable Dr. David Westenberg of the Missouri University of Science and Technology joins the #QualityQuorum to discuss his efforts at microbial outreach from K-12 (and beyond), his fascinating research program, and his experiences teaching microbiology to engineers.
Host: Mark O. Martin
Guest: David Westenberg
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Links for this episode A TEDX talk by Dr. Westenberg. An overview of the BioBuilder program. An overview of the iGEM program. Dr. Westenberg’s page on the Howard Hughes Medical Institute Biointeractive website. An article about “agar art” with microbes, featuring Dr. Westenberg. An article about the Woods Hole Microbial Diversity course by Dr. Westerfield. An article that shows Dr. Westernberg’s approach to teaching in a fun and accessible manner. Dr. Westenberg’s faculty website. Dr. Westeinberg’s laboratory group websiteIntro music is by Reber Clark
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Today, Dr. Mohammad Moniruzzaman, Assistant Professor at the Rosenstiel School of Marine, Atmospheric, and Earth Science at the University of Miami joins the #QualityQuorum to discuss his laboratory group’s work investigating a remarkable group of giant viruses and how they can shape marine algal community structure.
Host: Mark O. Martin
Guest: Mohammad Moniruzzaman
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Links for this episode Here is a recent review of the giant viruses (more information appears almost monthly!). Another overview of giant viruses. An even more recent review of the giant viruses. An article exploring what we do not know about giant viruses. A video about giant viruses. An interesting article relating giant viruses to early cellular evolution. An article exploring the involvement of giant viruses in the evolution of the eukaryotic nucleus? A report of endogenous giant viruses making their own genomes part of marine green algae. The preprint of an article discussed by Dr. Moniruzzaman. An article about finding giant viruses in very hostile underwater brine pools—the giant viruses are ubiquitous! An article about Dr. Moniruzzaman’s research. A video by Dr. Moniruzzaman. Dr. Moniruzzaman’s faculty website. Dr. Moniruzzaman’s research laboratory websiteIntro music is by Reber Clark
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Today, Dr. Jennifer Goff of the Department of Chemistry at SUNY College of Environmental Science and Forestry joins the #QualityQuorum to discuss her laboratory’s work studying the relationship between microbes in metal, as well as her path in the microbial sciences.
Host: Mark O. Martin
Guest: Jennifer Goff
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Links for this episode A fine remembrance of Carl Woese from the journal Nature. A wonderful book by the great David Quammen that emphasizes the impact Carl Woese had on biology. An article by yours truly on the impact Carl Woese has on my students. An overview of biogeochemistry. The carbon cycle and how the microbial world is involved with the process. The nitrogen cycle and how the microbial world is involved with the process. An article about tellurium and microbes. An older overview of how microbes are involved in mining, as well as a more recent article on that topic. A review of metals and microbes. Dr. Goff’s faculty website. Dr. Goff’s fascinating laboratory group website, including links to the papers discussed by Dr. Goff.Intro music is by Reber Clark
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Today, Dr. Justine Debelius of the Johns Hopkins Bloomberg School of Public Health joins the #QualityQuorum to discuss her fascinating work relating the human microbiome to nasopharyngeal cancer, as well as her path in the microbial sciences.
Host: Mark O. Martin
Guest: Justine Debelius
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Links for this episode A video overview of the human microbiome for introductory MIcronauts. Another interesting video introduction to the human microbiome. A review article describing relationships between microbiome and disease in general. A review article describing possible links between the microbiome and some forms of cancer. A short video describing possible links between the microbiome and some forms of cancer. An overview of nasopharyngeal cancer. A link to the article by Dr. Debelius on the relationship between the microbiome and NPC. Some updated information on this relationship. Dr. Debelius’ faculty scientist website.Intro music is by Reber Clark
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Today, Dr. Michele Swanson, Professor of Microbiology at the University of Michigan, joins the #QualityQuorum to discuss the her journey to microbiology, the mysterious disease causing bacterium Legionella, and how to best create a better scientific ecosystem.
Host: Mark O. Martin
Guest: Michele Swanson
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Links for this episode An overview of Legionella and its ability to cause disease from the Centers for Disease Control. A more formal overview of Legionella and Legionnaire’s Disease. An overview of Legionella as an interesting microbe. A review article by Dr. Swanson and colleagues about Legionella. A review article by Dr. Swanson and colleagues about Legionella’s life cycle. A history of Legionnaire’s Disease. An article about the Flint, Michigan outbreak of Legionella related disease. An article describing how Legionella can use amoebae as hosts, and how that can relate to disease. An article by Dr. Swanson and colleagues about the Flint, Michigan outbreak of Legionella. A link to the NIH Advisory Committee to the Director Working Group on Re-envisioning NIH-supported Postdoctoral Training, Dec 2023 The Frontline “Flint’s Deadly Water” documentary. A link to the NASEM’s 2020 report “Management of Legionella in Water Systems” A video interview with Dr. Swanson. Dr. Swanson’s faculty page. Dr. Swanson’s laboratory page. Dr. Swanson’s Wikipedia page. Dr. Swanson coauthored a fine textbook on microbiology. Dr. Swanson is a cohost on the This Week in Microbiology podcast.Intro music is by Reber Clark
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Today, Dr. Will Ratcliff of the Georgia Institute of Technology joins the #QualityQuorum to discuss the fascinating work his group has done exploring the evolution of multicellularity, and the wonderful example of “snowflake yeast.”
Host: Mark O. Martin
Guest: William Ratcliff
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Links for this episode A video of a #LuxArt workshop that Dr. Jennifer Quinn and I organized at an ASMCUE conference a few years ago. Such creativity! Here is a nice editorial overview of the issue of the evolution of multicellular versus unicellular life and how the latter could lead to the former. Here is a review essay on the topic of the evolution of multicellularity from Dr. Ratcliff’s laboratory group. A very recent and interesting review article exploring the possible “black swan” event leading to multicellularity in evolution. A foundational journal article on snowflake yeast from Dr. Ratcliff and research colleagues. A nice video of the snowflake yeast described by Dr. Ratcliff. A wonderful ‘must read” essay on the topic of snowflake yeast from Quanta magazine. A wonderful ‘must read” essay on the topic evolving multicellularity from Quanta magazine. A wonderful ‘must read” essay about the possibility of multicellular prokaryotes from Quanta magazine. A really engaging video about the evolution of snowflake yeast from Dr. Ratcliff. Dr. Ratcliff’s faculty website. Dr. Ratcliff’s quite fascinating laboratory website. A must read! Dr. Ratcliff’s outreach website. Another must read!Intro music is by Reber Clark
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Today, Dr. Margaret McFall-Ngai of the California Institute of Technology, joins the #QualityQuorum to discuss her philosophy of the future of biology. Dr. McFall-Ngai has been described as “…a recognized thought leader regarding the cornerstone role microbiology plays in the life sciences.” I could not agree more.
Host: Mark O. Martin
Guest: Margaret McFall-Ngai
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Links for this episode For beginning #Micronauts, I suggest this overview of the amazing roles microbes play in the lives of animals and plants: “We are living in a bacterial world, and it’s impacting us more than previously thought“. Here is the more advanced article coauthored by Dr.McFall-Ngai on this topic: “Animals in a Bacterial World.” A must read. A video on this topic by Dr. McFall-Ngai. Another video on this topic by Dr. McFall-Ngai. A wonderful review of the squid-Vibrio symbiosis (relevant to discussion) from the laboratory of Dr. Karen Visick. The TCT story: how the same signal creates a light organ in squid and disease in humans. PAMPs versus MAMPs as a paradigm shift. A wonderful profile on Dr. McFall-Ngai An essay about career building by Dr. McFall-Ngai. Margaret McFall-Ngai’s faculty website. The McFall-Ngai laboratory website.Intro music is by Reber Clark
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Today, Dr. Mark Mandel, Professor of Medical Microbiology & Immunology at University of Wisconsin-Madison, joins the #QualityQuorum to discuss the research his laboratory group does exploring how the luminous bacterium Vibrio fischeri finds its way into its symbiotic partner, the Hawai’ian Bobtail squid Euprymna scolopes. It will be an enlightening podcast!
Host: Mark O. Martin
Guest: Mark Mandel
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Links for this episode A video for introductory #Micronauts about the squid-Vibrio symbiosis featuring science journalist Ed Yong and two founders of the field, Dr. Ned Ruby and Dr. Margaret McFall-Ngai. An engaging video about Euprymna scolopes, the larger partner in this symbiosis, described by Dr. McFall-Ngai. A more advanced overview to this field, authored by Dr. Ned Ruby, Dr. Eric Stabb, and Dr. Karen Visick. A very complete recent review of the field from Dr. Visick’s lab. A video presentation by Dr. Mandel about this symbiosis. The first paper discussed by Dr. Mandel: “Hybrid Histidine Kinase BinK Represses Vibrio fischeri Biofilm Signaling at Multiple Developmental Stages.” The second paper discussed by Dr. Mandel: “High Levels of Cyclic Diguanylate Interfere with Beneficial Bacterial Colonization.” The third paper discussed by Dr. Mandel: “Mobile-CRISPRi as a powerful tool for modulating Vibrio gene expression.” Dr. Mandel’s faculty website. Dr. Mandel’s laboratory websiteIntro music is by Reber Clark
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Today, Dr. Roberto Kolter, Emeritus Professor of Microbiology at Harvard University (and past President of the American Society for Microbiology), joins the Quality Quorum to discuss his life long interest in microbes and microbiology, and how best to present microbiology to the public.
Host: Mark O. Martin
Guest: Roberto Kolter
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Links for this episode A wonderful article about the complexities of how microbes look and grow with live graphics. I use this article with my introductory #Micronauts every Fall. Beautiful! An article by Dr. Kolter discussing how to choose a study problem in microbiology…and other areas. The book “Life at the Edge of Sight” by Dr. Roberto Kolter and Dr. Scott Chimileski is very much worth your time. Highly recommended. Dr. Scott Chimileski’s website, with beautiful photographs of bacterial colonies. An article on the history of microbiology by Dr. Kolter. The article by Dr. Kolter I discussed during the podcast, “Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology.” A lecture by Dr. Kolter and Dr. Chimileski at Harvard University Museum of Natural History. Another lecture at the Harvard University Museum of Natural History by Dr. Kolter and Dr. Chimileski. Images from the “World in a Drop Exhibition” can be found here. An essay from “Small Things Considered” on abortive transduction, discussed in the podcast. Here is another essay on that topic. A biography of Dr. Kolter. Dr. Kolter’s laboratory website with many interesting links.Intro music is by Reber Clark
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