Finding Genius Podcast

Podcast Categories: Viruses

Immunology and COVID-19: Michael Betts Explains Immune Cell Responses to COVID_19 and Others
Michael Betts and his lab have focused on recoverable viruses like influenza and those that never leave human bodies like HIV. He explains different mechanisms of responses as well as what’s been unusual about our immune system and COVID-19.

He describes
- How initial human immune system responses are similar across viruses,
- How our bodies are able to clear some viruses and not others and examples of each, and
- What unusual and specific immune cell activities they’ve observed thus far with COVID-19.
Michael Betts is a professor of microbiology at the Penn Institute for Immunology. His lab studies human-specific responses to viruses. He begins by explaining the immune system in general from a microbiologist perspective. He comments that our initial response to most viruses of lethargy and fever is pretty similar. This is an active phase to eliminate the virus if possible.

He adds that with viruses like HIV, your body is not able to eliminate the virus. He explains in what ways the virus replication is always a step ahead and how its high replication rate is an advantage for the virus. He provides other examples, like the ability of CMV to encode an MHC complex decoy to evade detection by the CD8+ T cells.

He also describes what the field of immunology has observed with COVID-19 and describes his lab work specifically. He says that the initial response is not different from other infections, but the continuing outcomes and manifestations of those outcomes run the gamut. They’ve focused on reactions of T-cells and the innate immune system, which is mediated by several types of cells like monocytes.

They are noticing that severe COVID-19 has an impact on the innate lymphocyte population. They are seeing very dramatic changes in cell surface protein expression and in the population of cells called neutrophils, namely an extreme elevation of these in the blood. The cell surface protein effect is most pronounced in people with severe disease, not mild or moderate, which means it may help gauge reactions and treatments.

To learn more, see his lab’s website, bettslab.org, or look him up and contact him. His Twitter account is @BettsLab.

Podcast: Play in new window | Download | Embed
June 4, 2020
Investigating the Human Virome with Frederic Bushman
Professor Bushman has been studying microbes since the early 80s and was involved in researching HIV pathogenesis, developing in vitro HIV integration that led to integration inhibitors for treatment.

He shares interesting details about viruses with readers, such as
- Different types of retroviruses and which type are part of the human genome,
- The pathogenesis of some viruses and the variety of phages, and
- His recent study involving the development of a baby’s microbiome and virome.
Frederic Bushman, Ph.D., is the William Maul Measey Professor and Chair of Microbiology at the Perelman School of Medicine at the University of Pennsylvania.

He shares with listeners how his own interest in the field developed and then begins by addressing ways we understand viruses as scientists consider efforts like gene therapy. For example, he explains that HIV integrates into the host cell, which is why it is so difficult to get rid of it. However, it does not act on the scale of endogenous retroviruses, which infect germ cells and expand into every bodily cell as we grow. He says that the human genome is composed of 8% viral genes from these viruses.

The conversation then turns to the microbiome, virome, and bacteria phages and he reminds listeners of the vast number of viruses in the world. In fact, he talks of a “dark matter” existence level of viruses that researchers are just beginning to try and investigate. While the public may mainly hear about viruses in terms of pathogenesis and gene therapy, their involvement in our world and evolution is complex and far beyond these issues.

He also talks about his findings about to be published in Nature. He and his team studied the development of a baby’s microbiome and found that at birth, a baby is without bacterial colonists. He explains how the microbiome develops alongside integrative prophages. For prospective students wanting to enter the field, he suggests trying to formulate a question that’s interesting, important, and answerable.

To find out more, he suggests searching his name and the term “virome.” In addition, his faculty page has links to some of his publications: https://www.med.upenn.edu/apps/faculty/index.php/g20001500/p2236488

Podcast: Play in new window | Download | Embed
May 27, 2020
On the Latest in the Emerging Field of Virome Research—Ken Cadwell, PhD—Recanati Family Associate Professor of Microbiology, Skirball Institute of Biomolecular Medicine at New York University
Recanati Family Associate Professor of Microbiology at the Skirball Institute of Biomolecular Medicine, Ken Cadwell, discusses the virome and how it relates to infectious and inflammatory diseases.

In this episode, you will learn the following:
- What exactly is a virome, where it is found, and what it is comprised of
- What a bacteriophage is, and the ways in which it can interact with bacteria to ultimately cause the production of certain toxins
- What the inherent drawbacks are of “shotgun” sequencing for metagenomics, and how to overcome them
Understanding the role of the virome in health is an emerging field of research. In fact, many people aren’t even familiar with the term ‘virome,’ which refers to the collection of viruses that inhabit living things, which of course includes humans.

Dr. Caldwell’s lab is focused on understanding the functional consequences of viral infections primarily through the use of mouse models and cultured human cells. Through a collaborative network, Dr. Cadwell’s team is also trying to make correlations with humans directly in order to examine how viral exposure changes in individuals with certain diseases, such as irritable bowel disease (IBD).

Dr. Cadwell explains the approach they take in determining what viruses are present in a particle sample, whether it be in a mouse model or the human gut. The approach involves sequencing everything that’s there…which means sequencing a lot of bacteria and bacteriophages, which are viruses that infect and replicate within bacteria. Dr. Cadwell says that about 90 to 95 percent of the viruses they sequence are identified as bacteriophage.

So, what comprises the remaining five to 10 percent of viruses? Although it’s a small percentage relatively, Dr. Cadwell explains that identifying these other viruses is of high interest because these are the viruses that infect animal cells directly, rather than bacterial cells. The team at Cadwell’s lab is interested in seeing what viruses are present in healthy people, and why.

Dr. Cadwell also shares some exciting new research findings that show the human immune system is capable of reacting to certain bacteriophages that are supposedly only inside bacteria, suggesting that researchers need to be paying a lot more attention to bacteriophages that don’t seem to directly infect animal cells.

Dr. Cadwell discusses a number of fascinating topics, including the norovirus (in mice and humans), symbiotic relationships between viruses and hosts and how they are similar to symbioses between humans and the human gut microbiome, why it’s difficult to define what constitutes a healthy microbiome, and so much more.

Tune in and check out www.cadwelllab.nyu.edu to learn more.

Podcast: Play in new window | Download | Embed
May 21, 2020
Giant Viruses Give the Big Picture Researcher Chantal Abergel Explains What Giant Viruses Show Us
Chantal Abergel studies giant viruses, which are a relatively new discovery. She tells listeners how the size offers new observations in virology.

She explains
- Why preconceptions of virus properties delayed their discovery,
- What functions and processes the larger size enables researchers to observe, and
- What these things may tell researchers about virus and cell coevolution.
Chantal Abergel is the Research Director of the French National Centre for Scientific Research (CNRS). She achieved her Ph.D. in Material Science in 1990 from Aix Marseille University.

Dr. Abergel co-founded the Structural and Genomic Information (IGS) Laboratory at the CNRS.

She specializes in a study new to virology, namely giant viruses. She tells listeners that their very size made them undetectable previously because of filtration measures assuming a certain size, which kept these viruses out of the literal scope of study.

Dr. Abergel shares many traits and processes of the families they’ve been able to identify thus far. For example, bigger viruses are more complex with genomes that can be as large as 2.5 million base pairs. She gives a bit of the history, telling listeners about the first giant virus discovery called the Mimivirus as well as the family she’s currently studying, the Pandoravirus.

Their size makes them easier to isolate and observe. Dr. Abergel and her colleagues are studying their relationship with amoeba and have observed processes such as the capsid opening and contents transferring into the cell cytoplasm. Some explains that some viruses divide up and reproduce in the cytoplasm and some transfer and unfold into the nucleus and use cell machinery to duplicate.

She shares many fascinating processes that have implications about giant virus evolution. For example, after causing the overexpression of nuclear proteins inside of amoeba to address the question of whether the viruses are really cytoplasmic replicators, they observed the transcription machinery was not in the virus capsid and the virus didn’t enter the cell nucleus to replicate.

Rather they observed proteins leaving the nucleus of the amoeba and going to the virus for transcription. She remarks that this implies that these viruses may have been independent of the cell and this is a demonstration of how they coevolved.

To learn more, see her lab web page at CNRS, http://www.igs.cnrs-mrs.fr/en/the-lab/?lang=en, and search for her articles, which include pictures of some of these recorded processes.

Podcast: Play in new window | Download | Embed
May 20, 2020
How to Impede the Coronavirus in Cellular Machinery: Frederic Bards Shares His Research
Researcher Frederic Bard has studied coronaviruses’ step-by-step entry and replication inside cells. He explains to listeners which stages are the most promising for interference.

Along the way, he describes
- The parasitic nature and structure of virus binding and replicating mechanisms,
- How the ph of the endosome enables viruses to enter the cytosol where the viruses’ RNA replicates, and
- The promising identification of the VCP spike protein that the virus binds with and efforts to inhibit it.
Frederic Bard is an adjunct associate professor in the Department of Biochemistry at Yong Loo Lin School of Medicine at the National University of Singapore and is part of the Institute of Cellular and Molecular Biology with the Agency for Science, Technology, and Research (A Star) in Singapore.

He explains to listeners about the importance of host genes for coronavirus replication.

He reminds us that viruses are parasites and need the machinery of a cell to replicate—he has researched different proteins and machines inside the cell that help the structure of viruses to replicate: if we can understand that, he says, maybe we can block replication.

He describes the two moments that show the most promise for disturbing this process, namely when viruses bind with spike proteins on the outside of the cell and when they enter the cytosol for the viruses’ RNA replication.

A few years ago, he published work identifying the VCP protein that coronaviruses bind with and is now researching the possibility of inhibiting that protein without hurting the cell.

That is part of the challenge, he explains—to make the cell a little bit sick to inhibit the virus replication but not enough to damage the cell and health of the person. Along the way, he explains cell mechanisms in response to viruses, how the structure of virus works with the endosomes and cytosol.

For more, see his lab websites with links to his publications and contact information: https://www.a-star.edu.sg/imcb/science/scientific-programmes/multi-modal-molecular-(m3)-biology and https://bch.nus.edu.sg/fredericbard.htm.

Podcast: Play in new window | Download | Embed
May 11, 2020
Viruses and Evolution: Current Research on How Viruses Adapt with Paul Turner
Professor Paul Turner specializes in the evolution of viruses. He shares how researchers conceive of and approach viruses today, including
- Understanding viruses as possible “took kits” for other organisms alongside their own evolution toward opportunity;
- The goals of his own lab, such as studying viruses as ideal forms in understanding evolutionary processes; and
- Phages (viruses that target bacteria) and their potential to replace antibiotics to treat bacterial infection.
Paul Turner is the Rachel Carson Professor of Ecology and Evolutionary Biology at Yale University.

In this conversation, he covers many key topics about viruses and virus RNA and how bacteria and viruses may coevolve.

He explains that there are numerous ways bacteria have taken genes and functions from viruses and incorporated them into the bacteria to enable a new opportunity for bacterial life to continue. Further, our human genomes are full of what are recognizably virus genes, or “ghosts of infections past,” and we’re still not clear how these genes may function.

He also covers the tremendous potential for phages to fight infection as antibiotics lose their effectiveness.

He talks about some of the roadblocks to this forward movement and how his lab is approaching this research as well as using viruses to better understand evolution as a process and examine pathogenic virus ecology.

Along the way he explains multiple current theories on viruses, virus RNA, and even touches on the exciting work in ocean genomics, a field that is able to look even closer at metagenomics. He also talks about the technology available, how now that scientists have more single-cell tools to study and examine viruses, he’s more optimistic that we can access the individual cell level to see variation in how certain cells interact with “free riders” like viruses.

For more, see his page at Yale University, https://medicine.yale.edu/profile/paul_turner/, and the Turner Lab page, https://turnerlab.yale.edu/.

Podcast: Play in new window | Download | Embed
May 6, 2020
Virions and Provirus, Oxygen and Algae: Forest Rohwer Talks Research on Viromes
Professor Forest Rohwer’s lab invented many of the methods to look at the virome, particularly the uncultured methods utilizing metagenomics.

In this podcast, he shares some interesting observations of virus ecology, such as
- The diverse types and stages of viruses inside humans and on our body,
- The differences in behavior of viruses in our cells and out and how that may connect to disease therapies, and
- His current research focusing on ecosystems of the human lung, specifically cystic fibrosis, and coral reef virus ecosystems.
Dr. Forest Rohwer is a marine microbiologist and microbial ecologist and professor of biology at San Diego State University. He discusses the complex behavior of viruses in humans, observations and findings that may lead to treating how virions affect cells and how scientists can manipulate that behavior in treatments for pathogenic viruses such as Covid19.

He explains that we humans have viruses and bacteriophage, retrovirus, herpesvirus, Torque Teno Viruses (TTV), and more: it’s a complex ecosystem. Our gut in particular is filled with phages attacking the bacteria and in symbiosis with bacteria.

He provides one example of bacteria in our gut that carry a lot of prophage, which they shed over time. These viruses will bind to the mucus of the gut and forma barrier that will kill bacteria invading our gut, thereby protecting their host.

These are the kinds of relationships that reveal this complex relationship.

He also talks about his current research into two different ecosystems, namely the human lung in relationship to cystic fibrosis and coral reefs in the context of increased algae due to decreased fish and diversity. He explains how the human and coral system studies both reveal virus behavior, namely how provirus and virions increase or decrease depending on oxygen levels.

He explains that this may provide insights for therapies for disease to manipulate virus presence.

This may be useful for pathogenic viruses such as Covd19.

For more, see his lab page at https://coralandphage.org/, where a copy of his book Life in our Phage World is available as a free download.

Podcast: Play in new window | Download | Embed
April 30, 2020
Global Virus Tracking by Science Consortium: One Health Institute’s Jonna Mazet Discusses their Work
UC Davis’s One Health Institute (OHI) focuses on problem-solving for emerging infectious diseases and conservation challenges to address global health issues.

Executive Director Jonna Mazet shares their Predict project’s current findings, including
- How they have discovered numerous viruses and more than a hundred different coronaviruses, the family to which COVID-19 (SARS CoV-2) belongs;
- How they identify high-risk transmission zones where people are working with animals in a especially stressful way that would cause virus spillover; and
- What risk factors they’ve developed to gauge the viruses themselves through the help of 70 different international researchers.
In addition to her work as Executive Director, Joanna Mazet is a Professor of Epidemiology and Disease Ecology at the UC Davis school of Veterinary Medicine. OHI has been working since 2009 to understand viruses that spill over from animals. For the COVID-19 version specifically, they’ve been using their Predict platform to help global communities predict, understand, and identify its spread.

OHI and their Predict project is especially looking ahead to prevention for future global health issues. She discusses the various approaches, from bringing together ministries of health, agriculture, and environment in countries with less resources to communicate and identify high transmission zones. She describes the factors they use to identify high risk zones and means for mitigation.

Dr. Mazet also describes the essential efforts to prevent future global health issues such as pandemics, including the need to understand as much about viruses as we do about bacteria. She explains that predicting a virus’s harm potential is more about its ability to jump to multiple host species rather than its relatedness to other harmful viruses.

In addition, they are testing species that weren’t the target host to understand SARS CoV-2 (COVID-19) better and figure out clues to help scientist fight other viruses.

To find out more, see the list of published literature on predict.global, where maps of their surveillance work with test results and affected species are also posted.

Podcast: Play in new window | Download | Embed
April 24, 2020
Viruses as the R & D Sector of Evolution: James Shapiro Talks about the Natural History of Viruses
Professor James Shapiro shares his thoughts with listeners on all things viral. In this exploration of molecular biology, he touches on
- Some of the intricacies and differences in how retroviruses versus other types of viruses behave and affect their hosts;
- How viruses are sources of new information for cells that may be useful to evolving organisms at critical junctures; and
- Why he’s studying the evolution of cancers in comparison to organismal evolution.
James A. Shapiro has been with the Department of Biochemistry and Molecular Biology at the University of Chicago since 1973. He has written several books, including Evolution: a View from the 21st century. He begins by explaining some of the genome editing virus interactions bring about, including in the virus and bacteria-as-host relationship. He describes the protection phages (viruses that inhabit bacteria) offer bacteria from protozoans, for example.

He adds examples of mammal and retrovirus interactions and genome editing, citing placental development as a result. These, he comments, are examples of how viruses introduce new elements into evolving organisms, leading to his virus-as-R & D analogy.

Dr. Shapiro also describes this as a one-way transfer system and notes that viruses are part of what we call the biosphere. They are vehicles for cells communicating with each other. On their own, they can’t do much, yet they can enact change on their hosts. He expands on some of this molecular biology phenomena and explains that viruses are sources of new information that may be useful to evolving organisms at critical junctions in evolution.

He also offers an exploration of cancer behavior and evolution. Cancer is so destructive, he says, because cellular behaviors are enacted that wouldn’t normally be, yet cancer uses normal evolutionary processes to change. He’s working on understanding cancer by comparing its evolution with organismal evolution and noting the parallels.

Finally, he discusses his theory of cellular cognition, and that in the near future, we will think about cells in a more systemic, cognitive way—ultimately learning about living organisms is really learning about how systems behave.

For more, see his lab website at http://shapiro.bsd.uchicago.edu/, which links to his research, books, and past blogs and articles.

Podcast: Play in new window | Download | Embed
April 20, 2020
Virus Vacations – João Marques, Department of Biochemistry and Immunology, Federal University of Minas Gerais – How Viruses Travel and Spread Throughout Populations
João Marques, Department of Biochemistry and Immunology, Federal University of Minas Gerais, provides an overview of
his research, discussing viruses and explaining RNA interference mechanisms, arbovirus structure, and more.

Podcast Points:
- How do viruses evade immune systems?
- What is RNA interference?
- What can we learn about viruses by studying mosquitos?
Dr. João Marques earned his PhD from the Brazilian Federal University of Minas Gerais. Dr. Marques’ work was centered on the interaction between viruses and select host immune responses.

Dr. Marques discusses his background and why he became so interested in viruses in particular, and devoted much of his study to them. As he explains, they are fascinating because as small as they are, they can still have immense power within species, when the right conditions are present.

He explains why he was interested in viruses, and how hosts recognize virus infections. Dr. João Marques began working with insects and focused some of his studies on the mechanism of RNA interference, a very important antiviral response for most animals.

Dr. Marques explains how some viruses are excellent at evading immune systems. He discusses HIV in particular and how it targets cells. Continuing, he explains acute infections, and how some viruses proliferate rapidly, jumping from host to host.

The research doctor explains how double-stranded RNA is involved in the process of virus life, and he discusses how systems seek to contain infection. Going deeper, Dr. Marques explains how the production of proteins plays a role in informing other cells that certain cells are infected.

The research doctor talks about some of his work and experimentation with mosquitos, explaining infection and how viruses grow. As he explains, there is much still to learn about viruses and infections, and there are many intriguing questions. Continuing his overview,

Dr. Marques provides in-depth information on how viruses spread, detailing how the goal of a virus is to grow to a high level but not kill the host. Going further, he explains how viruses may appear, and how viruses that infect humans may have previously been solely mosquito viruses.

This virus evolution is a complex process, but it appears to be happening, though more research needs to be done to confirm theories.

Wrapping up, the virus expert talks about signature viruses that can tell us a lot about specific biology. He talks about density issues and how viruses within mosquitos mutate.

Podcast: Play in new window | Download | Embed
April 16, 2020

Accessibility Close Menu

Accessibility menu

Accessibility menu

Accessibility menu

× Accessibility Menu CTRL+U

Toggle enhanced keyboard navigation

Big cursor is enabled

Contrast + Invert Colors Dark Contrast Light Contrast

Bigger text is enabled

Desaturate colors is enabled

Underline links is enabled

Highlight Links

Legible fonts is enabled

Reset All