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Copyright: © Richard Jacobs
Returning guest Shiraz Shah specializes in bioinformatics. He uses microbial data analysis to uncover the complex and fascinating relationships between viruses, bacteria, and chronic conditions like childhood asthma. This conversation serves as part of a series in preparation for Richard's upcoming book on viruses, and Shiraz Shah shares his unique and valuable perspective on viral structure and functions gleaned from years of cutting-edge analysis. Topics include
Shiraz Shah is a senior researcher at the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC). Much of his graduate work focused on CRISPR-Cas9 bioinformatics. His current work involves analysis of data regarding bacteria hosts and viruses in the gut microbiome in particular. He explains how this analysis works at the level of genomics; for example, a virome sequencing might be compared to numerous other protein sequences in a search for significant patterns. COPSAC plans to take this collection of virus and bacteria data and follow the cohort of children for any corresponding organisms that might indicate causes or preventions of childhood asthma.
This opens up into an enlightening conversation about the complex role of phages, which are viruses that use bacteria as their host cell. Viruses are everywhere, Dr. Shah asserts, and he believes our old view that viruses are predominantly dangerous, mostly causing sickness, is outdated. Most of us and the kids COPSAC studies are full of viruses without any sickness. So, what are those viruses up to? Replicating. And that effort makes for a sometimes commensal or mutualistic host relationship. Dr. Shah explains that scientists see a lot of prophages that are maintained over several generations and kept by bacteria because they help the host bacteria. He and Richard bring up examples involving cancer and cholera, where a phage's presence changes the bacterial response in a human body in numerous ways, sometimes beneficial or commensal, and sometimes towards more virulent behaviors. Dr. Shah and Richard also debate the level of intent, signaling, and quorum-sensing abilities of viruses. Near the end of their conversation, Dr. Shah explains that his present work, called viromics, may have as a significant impact as metagenomics. In a few years, scientists may therefore have a completely different and exciting view of viruses. Listen in for an expert's view of this new type of foundational research.
For more about Shiraz Shah, see his page at COPSAC: copsac.com/home/about/staff/shiraz-shah/. Available on Apple Podcasts: apple.co/2Os0myK
In this podcast, returning guest and computational biologist and author Eugene V. Koonin and Richard examine intriguing angles of virus behavior. Dr. Koonin is a contributor to Richard's upcoming book on viruses, and Richard sees him as a cornerstone of his own biological knowledge. An expert on the origin and evolution of life, Dr. Koonin graces listeners with fascinating ideas, such as
Eugene V. Koonin is a senior investigator at the National Center for Biotechnology Information (NCBI), the National Library of Medicine, and the National Institute of Health. He's the author of several books, including Logic of Chance: The Nature and Origin of Biological Evolution. One of a series where Richard interviews contributors to an upcoming book, this conversation explores Dr. Koonin's early days of studying virology and how far science has since come in understanding the machinations involved. It was, in fact, his first studies on virus genomes and trying to decipher those codes that lead him into his present focus on computational biology.
Richard steers him towards several important questions on the nature of viruses and this gives Dr. Koonin opportunities to speak on some of their most surprising characteristics. He asserts that viruses are an intrinsic part of the biological realm and have their own evolutionary fate or trajectory; in other words, they experience their own selective factors that in turn shape their evolution. In this sense, he adds, they are substantially independent from their host; however, they are also completely dependent on their host for energy production. Therefore, they have same characteristics of life and yet are missing others. It is the tension in this mix of evolutionary force and obligate nature that makes them worthy of such discussions. Listen in to enjoy this intelligent entry into virus behaviors.
For more about his work, search his name in science publication aggregates and see his website at NCBI: ncbi.nlm.nih.gov/research/groups/koonin/. Available on Apple Podcasts: apple.co/2Os0myK
Without glycogen, we couldn't go very far. Dr. Sullivan is a specialist in the glycogen molecule, which stores glucose, our energy source. In this podcast, he describes exciting discoveries and future research centered on glycogen presence that might help explain the connection between diabetes and kidney disease. Listen and hear answers to these questions and more:
Mitchell Sullivan is pursuing a postdoc at the University of Queensland in a group that investigates glycation, diabetes, and how diabetic bodily systems handle extra glucose. Dr. Sullivan in particular follows glycogen formation in the organs. He's just setting out on a new study connecting diabetes and kidney health by focusing on glycogen presence in the kidneys of diabetics. Normally, glycogen is in the liver and muscle tissue, waiting to supply us with different kinds of energy needs. But microscopy shows glycogen in the kidneys of diabetic patients that likely leads to damage and inflammation. The findings may lead to better therapeutics and prevention measures, from a more effective diabetes and kidney disease diet to medical interventions.
Listeners will have the privilege of hearing straight from Dr. Mitchell the hypothesis for this study that's just begun. He explains with clarity why the structure of this glycogen in diabetic kidneys differs from its normal form and is significantly insoluble in this form. Furthermore, it sticks together in clumps of starch-like granules in the thick ascending limb of the nephron. He's investigating if these cells that aren't accustomated to glycogen become overwhelmed and the glycogen gets stuck, leading to damage and inflammation that make for one of the common kidney failure causes. What's most interesting is that his PhD work on glycogen in the liver and muscle tissue of diabetics makes this hypothesis seem more likely. Listen in to hear why that's the case and more about this study that might bring scientists that much closer to improving diabetes and kidney health.
To find out more about Dr. Mitchell's work, search his name in research aggregates, see his information page with Queensland University, and feel free to email him: mitchell.sullivan@mater.uq.edu.au. Available on Apple Podcasts: apple.co/2Os0myK
Dr. Reid specializes in host pathogen interactions studies such as investigating the chikungunya virus infection and Ebola virus microbiology. A returning guest, he and Richard discuss all things virus in this episode as Dr. Reid will contribute to Richard's upcoming book on viruses. Their conversation covers
St. Patrick Reid is an assistant professor in the Pathology and Microbiology Department in the University Of Nebraska Medical Center College Of Medicine. In a previous podcast, he and Richard discuss chikungunya diagnosis and pathology and Ebola virus symptoms and behavior. He begins this discussion explaining his journey into the field, which includes exciting postdoc work in France on Ebola. Now his researcher involves host pathogen interactions and he's particularly interested in different host proteins a virus has to recruit to replicate.
The conversation takes a turn into exploring what scientists have assumed about viruses compared to recent discoveries that may take that knowledge in new directions. For example, he talks about ancient phage discoveries in glacial bacteria and phage-bacteria coevolution. He describes an interest in how viruses that infect bacteria allow those bacteria to live in a community of other bacterium. The viruses actually play a role in enabling those bacteria to survive. He discusses numerous other virus characteristics and implications, from DNA versus RNA viruses and what that dictates regarding habits like latency. He also addresses when that understanding changes with new discoveries, such as finding Ebola virus in chimps months after infection. They also talk a little virus philosophy and cover topics like what enables virus entry into cells and how tropism works.
For more about Dr. Reid and his work, see his website at the university, unmc.edu/pathology/faculty/bios/reid.html, and follow him on Twitter as @StPatrickReid3. Available on Apple Podcasts: apple.co/2Os0myK
While Dr. Jospeh Masci could speak on numerous specific issues in the realm of infectious diseases microbiology, today's discussion centers on a general exploration of virus behaviors and characteristics. In this podcast, he addresses
Joseph R. Masci is a clinical professor of Medicine, Infectious Diseases, Environmental Medicine and Public Health, and Global Health at Mount Sinai. His expertise includes HIV/AIDS diagnosis and treatment, general infectious diseases, tropical medicine, and emergency preparedness. He's currently coauthoring a book with Richard about viruses. He begins by describing how he was inspired by the infectious disease faculty in medical school and went on to work in the area, meeting the AIDS crisis and bioterrorism concerns post 9/11, and now is heavily focused on investigating COVID-19. The conversation turns into speculations about whether viruses should be considered alive and if that designation ultimately maters. This opens up a deep dive into virus behaviors.
One particular characteristic that varies by virus and therefore effects infectious disease treatment is latency or the dormant stage. He discusses how such a period is quite common in many viruses, commenting that HIV can have long latency while cold viruses might hold dormancy for only a day or two. He connects this with how the virus takes hold in human cells and why this timing differs according to the virus mechanisms. They also discuss what factors dictate virulence and when passage from human to human increases or decreases the virulent attributes with specific examples. He adds that it's important to consider what the host contributes to the interaction as well as other organisms and compounds. The discussion also delves into virus origins, the nature of bacteria and virus coevolution, signaling between viruses, and the possibility of viruses working together with job-specific attributes.
For more, see his NIH work and his website at Mount Sinai: mountsinai.org/profiles/joseph-r-masci. Available on Apple Podcasts: apple.co/2Os0myK
The COVID-19 situation isn't the first of its kind—not entirely, at least. For as many times as you've heard voices claiming it's triggered the "new normal," you should have also heard the voices of reason and evidence and logic, which assert that it's really more like an old normal, yet one that is causing unprecedented levels of damage to the underpinnings of society. Why haven't you heard these voices? Because they've been censored and suppressed by those who stand to gain by spreading fear and lies. Press play to learn the following:
Ken McCarthy, a pioneer in the movement to commercialize the internet, an expert on internet advertising and marketing, and former student of neuroscience at Princeton University, presents an eye-opening look at COVID-19 in the context of global history. It's one you won't hear on the news, and for good reason, which McCarthy explains in depth. This explanation leads to so many others, such as how to develop and inseminate brilliant propaganda, what it takes to actually implement a war, what it means to put a human being on a ventilator, how to understand the Nuremberg Code in the current context of COVID-19, the truth about Bill Gates' record as a businessman, the surprising role in and influence on bioethics wielded by Christine Grady, Anthony Fauci's wife, the very real prospect of digital IDs as vaccine schedule verification, the important distinction between central and commercial banks, and more.
Visit kenmccarthy.com for more information. Some Important Links to Explore: Fauci's First Fraud: https://www.youtube.com/watch?v=wy3frBacd2k&feature=emb_logo The New York Problem: https://www.youtube.com/watch?v=qXD1UR2dmZ0&feature=emb_title Ken McCarthy's top CoVid videos: https://www.brasscheck.com/video/the-covid-con-dismantled/ Ken McCarthy's top Brasscheck videos: https://www.brasscheck.com/video/the-hiv-aids-fraud-dismantled/ Available on Apple Podcasts: apple.co/2Os0myK
This is a unique show in the Finding Genius series. Podcast founder and host Richard Jacobs sites Perry Marshall's ideas as the impetus for starting the Finding Genius podcast. In this discussion listeners can learn more about why and hear about an upcoming symposium Marshall has helped construct on cancer and evolutionary biology. He explains
Perry Marshall is an author and highly influential business consultant with an electrical engineering background. In this discussion, he connects the foundational ideas in Evolution 2.0 with cutting-edge cancer science. Marshall lost his father to cancer at age 17 and has followed theories behind its treatment ever since. He reminds listeners that common cancer therapy treatment only works routinely with early stage cancer. Alternatively, he says that when cancer reaches stages 3 and 4, survival chances are not that much better than they were in 1930. Therefore, there must be a lag in how we are addressing serious cancer diagnoses. This lag is connected with a traditional view of passive evolutionary theory rather than theories like that of Professor Henry Heng, who claims evolution is actively engineered by organisms themselves; in addition, they are able to pass those engineered traits to their offspring.
Henry Heng is one of the speakers at the upcoming Cancer and Evolution Symposium along with Columbia University Medical Center's Azra Raza and evolutionary theorist James Shapiro from the University of Chicago. Dr. Heng connects this theory of evolution and cancer, noting that treatments like chemo destroy about 98% of the cancer cells while the few remaining develop massive wholesale restructuring of their DNA and are then more equipped to spread and survive. Importantly, this restructuring is active rather than a random accident of mutations. Marshall explains these ideas in more detail and discusses other topics covered by the speakers. He describes the symposium as a world-class collection of cancer and evolutionary theorists coming together to address cancer evolution and disable the cancer treatment lag. The symposium will work via Zoom and takes place October 14th through 16th.
To sign up and learn more, see the symposium website: cancerevolution.org. Available on Apple Podcasts: apple.co/2Os0myK
Dr. Anderson' research focuses on the interaction between genetics, evolutionary biology, and tropical diseases. He works with the two most dominant parasites that infect humans and cause particularly high mortality in children: those species that cause malaria and schistosomiasis. In this podcast, he discusses
Tim Anderson is a professor and co-leads the Disease Intervention and Prevention Program at Texas Biomedical Research Institute in San Antonio, Texas. He helps listeners understand the basics of how genome sequencing techniques are used to determine relatedness and other factors in parasites that can then help scientists understand their life cycle, population genetics evolution, and how drug resistance develops and might be combatted. He works specifically in the Myanmar border region but discusses the differences in infection rates between areas to explain parasite infection characteristics. For example, they've found that people who get bit very rarely tend to get extremely sick whereas there seems to be some immunity in areas of higher infection bit rates. However, ultimately, this translates to a U-shaped mortality between these two extremes and he explains why.
Dr. Anderson also discusses some important work by colleagues and how these different areas of research come together to create a greater understanding of parasite activity. He describes what drug resistance looks like and gives several examples as the resistance mechanics varies with the action of the drug. After explaining the basics in more detail and some exciting finds, he describes his end goal as to better understand the evolution of drug resistance alongside the fitness cost of drug resistant genes. This has progressed to following how parasites eventually get around those fitness costs.
For more, see his information page, txbiomed.org/scientists/timothy-j-c-anderson/, and search his name in PubMed for publications. Available on Apple Podcasts: apple.co/2Os0myK
In one line of research, Professor Levi Morran observes the coevolution of C. elegans strains and microbial pathogens through population level biology to ask how and why sex evolved and why it is maintained. This is part of his overall research into how genetics and evolution affect the interaction of hosts and microbes. In this podcast, he explores
Levi Morran is an assistant professor of biology at Emory University and is interested in factors affecting adaptive evolution. His lab utilizes experimental evolution, which means they perform evolution experiments in real time with genetics biology and evolution biology. They mostly use particular strains of C. elegans, which go through several generations quite rapidly. He explains this with a concrete example: when his lab explored the antagonistic interactions between a host and microbes and the influence of the evolution of sex, they set up populations of C. elegans that would produce sexually and through self-fertilization. They found that the self-fertilizing populations did not adapt to the pathogens and mostly died out. He explains why he thinks this happened and how they may explore this further.
He also explores general benefits of experimental evolution and the advantages it offers researchers such as the ability to control and spin factors that can address very specific questions in certain conditions. He adds that conditions in nature are quite different, yet these experimental studies can point evolution theory in helpful directions. In addition, he explains the level of considerations an experimental evolution study must undertake, from seeking and using specific strains of nematodes fitting what the experimental questions ask, to unlocking characteristics in those nematodes to produce populations that will undergo, for example, sexual reproduction. He also addresses issues of microbiomes in nature versus the lab and questions regarding epigenetics.
For more, see his lab's website: wormlab.wordpress.com. Available on Apple Podcasts: apple.co/2Os0myK
Dr. Oliver Schacht says that antimicrobial resistance (AMR) is a serious pandemic that needs as much attention as COVID-19. In fact, 700,000 people now die annually across the globe from AMR infections. In this podcast, he addresses
Oliver Schacht, Ph.D., is the Chief Executive Officer for both OpGen and Curetis and is an expert in the molecular diagnostics industry. He addresses causes of antimicrobial resistance and antibiotic resistance mechanisms, but spends the majority of the podcast explaining why it is a world-wide issue and what solutions are available now and in the near future. At the center of these solutions lies the need to identify the species of antibiotic resistant bacteria and its resistance factor quickly. This means better, faster testing to insure more accurate treatment and less over prescription of broad spectrum antibiotics.
He adds that using broad spectrum antibiotics aggressively to fight undiagnosed infections leads to effective and rapid evolution of bacteria towards resistant adaptations. He says that if we keep using these broad spectrum antibiotics, some projections predict that by the year 2050 we may have 10 million deaths a year from these infections globally. He details the history of testing and explains why the technology has lagged. In a nutshell, we're still doing what we have been doing for 150 years, which requires significant time for cultures to grow and test.
He then explains how OpGen and other companies are developing rapid PCR tests as well as faster and better next generation sequence testing. He predicts the cost and timing for these will continue to decline and that will only improve the quality and helpfulness of the testing. Finally, he carries a global theme throw this discussion, explaining that this issue is analogous to climate change alleviation: there's not a simple fix and the issue can't just be handled locally—this requires a global approach to be effective. Listen in for more details and discussion about these issues.
For more, see the company's website at opgen.com. In addition, they are active in all social media outlets. Available on Apple Podcasts: apple.co/2Os0myK
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