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  • Discovering Fossilized Microbes in Antarctic Ice Cores With Manuel Martinez Garcia

    Discovering Fossilized Microbes in Antarctic Ice Cores With Manuel Martinez Garcia
    2025/03/14
    Manuel Martinez Garcia, Ph.D., a professor of microbiology in the Physiology, Genetics and Microbiology Department at the University of Alicante in Spain, paints a picture of what microbial life looked like thousands of years ago by analyzing microbial genomic signatures within ice cores collected from the Antarctic ice shelves in the 1990s. Links for the Episode New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves – mSphere paper. Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles – Nature communications article. Manuel Martinez Garcia’s Lab website. How stable is the West Antarctic Ice Shelf? – Press Release from Alfred Wegener Institute.Take the MTM listener survey! Watch this episode: https://youtu.be/CHCMO74_gIY Ashley’s Biggest Takeaways There is a unique habitat beneath Antarctic ice shelves, where microbes live without light and rely on unusual energy sources. Ice cores from these Antarctic ice shelves can preserve fossilized genomic records of microbial life from long ago. Comparing past and present samples can help us understand how microbial life is responding to environmental stressors, like temperature changes and acidification, over time.It can also provide key insights to changes in biodiversity. Featured Quotes: Motivation for the Research Ice shelves are like massive floating ice that are in Antarctica, mainly. They can be as big as, for example, France, the country. So, they are super big—they are enormous. And they can be as thick as, let's say, 1000 meters. So, this is a massive [piece of] ice that we have in our planet. And beneath that massive ice, we can have a very peculiar and a special habitat in which microbes live without light. They have to manage, to thrive and reproduce, without using a standard energy like we have on the surface of the sea or in the forest, where we have light that is driving and providing the energy for the ecosystem. But in this case, these ecosystems are totally different. [The ice shelves] are deep and interconnected. Basically, there are different oceanic currents, for example, there is one Circumpolar Current that surrounds Antarctica, and there are also other currents that basically go from the bottom to the surface, moving, you know, all the water masses. The interesting part of this story is that every single second in our lives, this sea that is beneath the platform, the ice shelf, is frozen over and over, and then we have different layers of antiquity that preserve the microbes that are living in the ocean. So, for example, let's say, 1000 years ago, the sea water was frozen, and then we can find a layer beneath the Antarctica ice shelf, where these microbes are preserved and frozen. Basically, it's like a record—a library of microbes, fossil records of microbes—from the past ocean, from 1000 years ago until present, more or less. And then we can go to these records, to these layers of frozen sea water, and pick these samples to somehow recover the genetic material of the microbes that were preserved and frozen 1000 years ago or 500 years ago, in the way that we can somehow reconstruct or build the genetic story of the microbes from the past, for example, pre-industrial revolution to present. We need to think that microbes sustain the rest of the food web. So, they sustain of the rest of life in the ocean. They provide carbon for the rest of organisms, the fishes, whales [and other] big animals that we have in our oceans. And if the microbes are responding in a way that is not satisfactory, or in the way that we think can maintain the food web, this is kind of scary. And this is what we are trying to do: we are trying to go back to the past and see how the microbes are changing [genetically]. Sample Collection We didn't collect the samples. [They were collected] back in the 90s, so, 40 years ago, by a German group led by the Alfred Wegener Institute, which is probably one of the most famous polar institutes in the world. They, basically, led an expedition, I think it was in 92, and they decided to go to this ice shelf in Antarctica, in the Filchner–Ronne Ice Shelf to collect these ice cores. And then the surprise was when they were progressing in the drilling, they realized that on the top part of the ice core was fresh water, meteoric snow that was compacted forming the ice. But they realized that below that part, there was a sea water that was frozen. And then they thought that these samples were very interesting, because they somehow store material from the past, and they shipped these samples to Alfred Werner Institute in Bremerhaven in Germany. And half of the samples were stored for 40 years until I decided to contact the Institute and to propose this research. And I basically contacted the director of the Institute, and also the group of Frank Wilhelm, to propose the idea. And basically...
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    49 分
  • Revenge of the Microbes With Brenda Wilson and Brian Ho

    Revenge of the Microbes With Brenda Wilson and Brian Ho
    2025/01/16
    Episode Summary Mother-Son duo, Brenda Wilson, Ph.D., professor of microbiology and the Associate Director of Undergraduate Education in the School of Molecular and Cellular Biology at the University of Illinois at Urbana Champaign and Brian Ho, Ph.D., researcher and lecturer at the Institute of structural and molecular biology, a joint institute between the Department of structural and molecular biology at the University College of London and the Department of Biological Sciences at Birkbeck University of London discuss the inspiration and motivation for their recent book, Revenge of the Microbes: How Bacterial Resistance is Undermining the Antibiotic Miracle, 2nd Edition, emphasizing the global nature of AMR and providing a unique perspective on what is needed to solve it. Ashley’s Biggest Takeaways: Dynamics surrounding the AMR crisis are complex and require an understanding of many different perspectives, including those of the farmers, health care professionals, pharmaceutical companies and individuals, in order to foster true and lasting global collaboration on the issue.Point-of-care diagnostics are critical to improving treatment decisions and reducing hospital costs.Better communication and education are needed in order to rebuild trust in scientists and institutions.Continuous research is necessary, as AMR will continue to evolve.Citizens are a key piece of the puzzle when it comes to pushing for change and supporting solutions to AMR. Featured Quotes: Wilson: “I'll start with actually my Ph.D., which is talking about bacterial antibiotic biosynthesis. And so, I did some work in that arena, but since then, I've actually been working on bacterial protein toxins. These are very potent eukaryotic modulators that when bacteria get into the host, they release these proteins that are very large, that are able to interact with very specific cells. They actually get inside the cells—into the cytosol—and then they affect various signaling pathways in the host that can go anywhere from killing the cell to modulating some of the processes that the cell undertakes, even differentiating them and causing cancer. So, one of my main focuses in my lab has always been to understand the structure and function of these toxins, to understand how they affect the eukaryotic cell system. And then now that we know a lot about them, we're actually moving more into the direction of trying to basically use them as biologics. We have some platforms that we call bacterial toxin inspired drug delivery, where we're using the mechanisms of how they work and their exquisite specificities to be able to actually use them for therapeutic applications.” Ho: “I got my start doing molecular genetics, actually, with John Mekalanos at Harvard, and I was kind of at the ground floor of the seminal work looking at the Type VI secretion system. And so, I got a front row seat to the kind of discovery and a lot of the initial understanding of the system. And I've kind of taken that work and expanded beyond it to look at kind of the ways different bacteria interact with each other within microbial communities. So my current work is looking at both DNA conjugation as well as the type six antagonism, and how the bacterial interactions kind of work together to build a larger population dynamics and interface with like the hosts that kind of house a your microbial communities.” Antimicrobial Resistance Wilson: “In 2005 [when the first edition of Revenge of the Microbes was written], there was very little activity or understanding about antibiotic resistance and how important it was. Outside of the field, doctors were encountering it. But oftentimes what was happening is they just said, ‘Oh, well, we'll just find another drug, you know.’ And pharmaceutical companies, they were recognizing that there was a problem, and they would go off trying to hunt for new ones. And then right around the late 90s, there was a big impetus, because they thought, ‘Oh, we, we have a miracle here, because we now do complete genomes. We can get out the comparative genomics and all the high throughput things, all the animations,’ and that this would lead to many more new discoveries. And I think the pharmaceutical companies were very disappointed, and they started backing out of what they deemed a huge commitment. Two decades later, people already were starting to get aware, at least in the field, and even the industry and the physicians. People were getting aware, but I think that they were stumbling, because of their silos, in trying to get interactions with each other. And I think part of it was that they felt that, ‘Oh, we can try to solve it ourselves.’ And in reality, this is a problem that that is concerning everyone, and everyone is contributing to it. Everyone has to find a solution to help, and we need to have more synergy. There have to be more interactions, and we have to do this at a much more global scale. And so that ...
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    52 分
  • Binning Singletons With Joseph James

    Binning Singletons With Joseph James
    2025/01/06

    Joseph James, biologist at the U.S. Environmental Protection Agency, discusses his career trajectory and the creation of Binning Singletons, a unique mentorship program built on peer-to-peer networking at scientific meetings and conferences and was first implemented in 2019 at ASM Microbe.

    Links for the Episode Binning Singletons and Peer-to-Peer Networking
    • Learn more about Binning Singletons.
    • Contact Joe James: Joe@binningsingleton.com
    • Follow Binning Singletons on Bluesky.
    • Binning Singletons: Mentoring through Networking at ASM Microbe 2019—mSphere article.
    • Binning Singletons: Tackling Conference Networking When You Don’t Know Anyone—Guest post on Addgene Blog.
    • Mastering a Mentoring Relationship as the Mentee—asm.org article that James says has really helped him explain Binning Singletons as a coaching form of mentorship.
    • Mapping a Mentoring Roadmap and Developing a Supportive Network for Strategic Career Advancement—article on developing networks of mentors, another area Binning Singletons tries to address.
    • #FEMSmicroBlog: Networking at Online Conferences (for Early Career Scientists).
    • Take the MTM listener survey!
    James’ Research
    • Dietary lead modulates the mouse intestinal microbiome: Subacute exposure to lead acetate and lead contaminated soil.
    • In situ differences in nitrogen cycling related to presence of submerged aquatic vegetation in a Gulf of Mexico estuary.
    • Quantifying stream periphyton assemblage responses to nutrient amendments with a molecular approach.
    • Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA Genes.
    • Use of composite data sets for source-tracking enterococci in the water column and shoreline interstitial waters on Pensacola Beach, Florida.
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    56 分
  • Biorisk Assessment and Management With Saeed Khan

    Biorisk Assessment and Management With Saeed Khan
    2024/11/11
    Saeed Khan, Ph.D., Head of the Department of Molecular Pathology at Dow diagnostic research and reference laboratory and President of the Pakistan Biological Safety Association discusses the importance and challenges of biosafety/biosecurity practices on both a local and global scale. He highlights key steps for biorisk assessment and management and stresses the importance of training, timing and technology. Ashley's Biggest Takeaways Adequate biosafety and biosecurity protocols depend on a thorough understanding of modern challenges, and scientists must be willing and able to respond to new technological threats appropriately.In the microbiology lab, the threat goes beyond the physical pathogen. Implications of genomics and cyber security must be built into biorisk management techniques, including data storage and waste management practices.Risk assessments involve evaluation of both inherent and residual risk.Inherent risk is linked to the pathogen.Residual risk varies according to the lab, equipment, employee, environment, etc.As a result, biosafety and biosecurity risks are constantly changing, and assessments must be repeated strategically and often.Khan recommended repeating a risk assessment whenever a key variable in the equation changes, i.e., new equipment, new employee, new pathogen. He also recommended (at minimum) conducting routine risk assessments every 6 months, or twice a year. Featured Quotes: “We need to have basic biosafety and biosecurity to stay away from these bugs and the modern challenges, like cyber biosecurity and genomics. These are the new areas, which are potential threats for the future, and where we need to train our researchers and students.” “Starting from simple hand washing or hand hygiene, the basic things we use are gloves, goggles and PPE to protect the workers, the staff and the patient from getting infected from the environment, laboratory or hospitals. These are the basic things, and it's very crucial, because if one is not using gloves in the lab or not wearing the lab coat, he or she may get infected from the sample, and the patient can get infected from the physician and doctors or nurse if they are not following the basic biosafety rules. These [things] are routinely important. Every day we should practice this.” “But there are [also] new challenges. Particularly in the microbiology lab, we [used to] think that once we killed the bacteria, then it's fine. But nowadays, it's not the way we should think about it. Though you kill the bacteria practically, it still has a sequence, [which] we call the genome, and if you have that information with you, you theoretically have the potential to recreate that pathogen… that can be used or maybe misused as well.” “[Working with] scripts of pathogens, like smallpox or the polioviruses, we call this synthetic biology. Different scientists are doing it for the right purposes, like for production of vaccines, to find new therapeutics, to understand the pathology of the diseases. But on [the other hand]—we call it dual use research of concern (DURC)—the same can be misused as well. That's why it's very important to be aware of the bugs that we are working with, and the potential of that pathogen or microbe, to the extent that can be useful or otherwise.” “So, we should be aware of the new concern of the technology, synthetic biology and DURC. These are new concepts—cyber, biosecurity and information security [are all] very much important these days. You cannot be relaxed being in the microbiology lab. Once we have identified a pathogen, declared a result to the patient and the physician, and it's been treated, we [still] need to be worried about waste management—that we discard that waste properly and we have proper inventory control of our culture. It should be safe in the locker or on in the freezers and properly locked, so we should not be losing any single tube of the culture, otherwise it may be misused.” Risk Assessment “The best word that you have used is risk assessment. So, it should gage the severity of the issue. We should not over exaggerate the risk, and we should not undermine the risk. Once the risk assessment been made, we can proceed.” “Right from the beginning of touching a patient or a sample of the patient until the end of discarding the sample, that is called biorisk management. It's a complete science that we need to be aware of—not in bits and pieces. Rather a comprehensive approach should be adopted, and each and every person in the organization should be involved. Otherwise, we may think [we are] doing something good, but someone else may spoil the whole thing, and it will be counterproductive at the end.” “We should involve each and every person working with us and the lab, and we should empower them. They should feel ownership that they are working with us, and they are [as] responsible as we are. So, this the whole process needs to be properly ...
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    50 分
  • From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier

    From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier
    2024/09/27

    Nicole Dubilier, Ph.D., Director and head of the Symbiosis Department at the Max Planck Institute for Marine Microbiology, has led numerous reserach cruises and expeditions around the world studying the symbiotic relationships of bacteria and marine invertebrates. She discusses how the use of various methods, including deep-sea in situ tools, molecular, 'omic' and imaging analyses, have illuminated remarkable geographic, species and habitat diversity amongst symbionts and emphasizes the importance of discovery-driven research over hypothesis-driven methods.

    Watch this episode: https://www.youtube.com/watch?v=OC9vqE1visc

    Ashley's Biggest Takeaways:
    • In 1878, German surgeon, botanist and microbiologist, Heinrich Anton de Bary, first described symbiosis as the living together of two or more different organisms in close physical intimacy for a longer period of time.
    • These relationships can be beneficial, detrimental or commensal, depending on the organisms involved.
    • Microbial symbiosis research holds great potential to contribute to sustainable energy production and environmental health.
    Links for This Episode:
    • Learn more about one of Dubilier's research vessels and see videos from the expidition.
    • Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.
    • Chemosynthetic symbioses: Primer.
    • Take the MTM listener survey!
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    31 分
  • When Proteins Become Infectious: Understanding Prion Disease With Neil Mabbott

    When Proteins Become Infectious: Understanding Prion Disease With Neil Mabbott
    2024/08/23

    From Bovine Spongiform Encephalopathy (BSE) to Creutzfeldt-Jakob disease (CJD), Neil Mabbott, Ph.D., has worked for nearly 2 decades on understanding the mechanisms by which prion proteins become infectious and cause neurological disease in humans and animals. He discusses the remarkable properties of prions and addresses complexities surrounding symptoms, transmission and diagnosis of prion disease.
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    56 分
  • Trillion Dollar Microbes Make the Bioeconomy Go Round With Tim Donohue

    Trillion Dollar Microbes Make the Bioeconomy Go Round With Tim Donohue
    2024/05/28
    Episode Summary Timothy Donohue, Ph.D.—ASM Past President, University of Wisconsin Foundation Fetzer Professor of Bacteriologyand Director of the Great Lakes Bioenergy Research Center (GLBRC) calls genomics a game-changer when it comes the potential of microbes to create renewable resources and products that can sustain the environment, economy and supply chain around the world. He also shares some exciting new advances in the field and discusses ways his research team is using microorganisms as nanofactories to degrade lignocellulose and make a smorgasbord of products with high economic value.

    Take the MTM listener survey! Ashley's Biggest Takeaways:
    • The bioeconomy can be broadly defined as the use of renewable resources, including microorganisms, to produce valuable goods, products and services.
    • Microbes have the potential to create products that cannot be made by existing synthetic chemistry routes.
    • Using raw, renewable resources to create a circular bioeconomy is beneficial to the environmental footprint, economic footprint and supply chain security around the globe.
    Links for This Episode:
    • The theme of our Spring 2024 Issue of Microcosm, our flagship member magazine is Microbes and the Bioeconomy: Greasing the Gears of Sustainability, launches this week and features an article based on this MTM conversation. If you are an ASM Member, check back on Wed., June 30 for the newly published content! Not a member? Consider renewing or signing up today, and begin exploring endless potential to boulster your career and network with professionals, like Donohue, in your field.
    • Get Bioeconomy Policy Updates.
    • Heading to ASM Microbe 2024? Check out this curated itinerary of sessions on the bioeconomy, including those discussing the use of algae for bioproduction and synthetic biology for natural product discovery.
    • Learn more about the Great Lakes Bioenergy Research Center.
    • MTM listener survey!
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    49 分
  • Rabies: The Diabolical Virus With Many Symptoms and Hosts With Rodney Rohde

    Rabies: The Diabolical Virus With Many Symptoms and Hosts With Rodney Rohde
    2024/05/07

    Rodney Rohde, Ph.D., Regents’ Professor and Chair of the Medical Laboratory Science Program at Texas State University discusses the many variants, mammalian hosts and diverse neurological symptoms of rabies virus.

    Take the MTM listener survey!

    Ashley’s Biggest Takeaways:
    • Prior to his academic career, Rohde spent a decade as a public health microbiologist and molecular epidemiologist with the Texas Department of State Health Services Bureau of Laboratories and Zoonosis Control Division, and over 30 years researching rabies virus.
    • While at the Department of Health Lab, Rohde worked on virus isolation using what he described as “old school” cell culture techniques, including immunoassays and hemagglutinin inhibition assays.
    • He also identified different variants of rabies virus, using molecular biology techniques.
    • Rohde spent time in the field shepherding oral vaccination programs that, according to passive surveillance methods have completely eliminated canine rabies in Texas.
    • In the last 30-40 years, most rabies deaths in the U.S. have been caused by bats.
    • Approximately 98% of the time rabies is transmitted through the saliva via a bite from a rabid animal.
    • Post-exposure vaccination must take place before symptoms develop in order to be protective.
    Links for This Episode:
    • Molecular epidemiology of rabies epizootics in Texas.
    • Bat Rabies, Texas, 1996–2000.
    • The Conversation: Rabies is an ancient, unpredictable and potentially fatal disease. Rohde and Charles Rupprecht, 2 rabies researchers, explain how to protect yourself.
    • The One Health of Rabies: It’s Not Just for Animals.
    • MTM listener survey!
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    55 分