Finding Genius Podcast

Founding director of the Center for Microbiome Innovation and professor of pediatrics and computer science & engineering at UC San Diego, Rob Knight, discusses several aspects of his past and ongoing contributions to the field of microbiome research. He also discusses his recent focus on the COVID-19 pandemic. On this episode, you'll learn the following: Why COVID-19 is causing a very time-sensitive need for serology tests to detect antibodies What dietary factors affect the microbiome in certain viral and bacterial diseases (e.g. salmonella, influenza) Why planting eucalyptus trees outside Australia was a terrible idea, and how this relates to pathogenic bacteria and microbial communities in the human gut Rob Knight helped develop the technology that enabled the field of microbiome research to get where it is today. For example, Knight's lab has developed software for microbiome analysis, lab protocols for looking at thousands of microbiomes simultaneously, and the American Gut Project, which analyzed hundreds of thousands of microbiome samples from humans to plants to soil and oceanic environments. He explains that while the human genome is fixed, the microbiome is constantly changing. The idea is that if it can be understood what causes or leads to changes in the microbiome, then it may be possible to control the microbiome in ways that confer health advantages. When COVID-19 began spreading globally, Knight was working on a project that aimed to determine the relationship between diet and the microbiome, and how it might make people more or less susceptible to disease. He's now carrying out this research with an eye towards the current pandemic, and hoping to identify whether there are dietary or supplemental interventions that can help people combat the virus, or prevent symptoms of the virus altogether. Knight is currently trying to develop technology that will allow for a broader, simultaneous view of the entire metabolome and microbiome, and the influence of diet upon them both. "In many ways, COVID-19 is providing a stress test of what we can do right now, which is going to be very useful for pointing the way towards what we need to develop over the next few years," says Knight. He continues by explaining the importance and challenge of being able to detect antibodies to COVID-19, as this would indicate whether someone has been exposed to the virus and is therefore likely to have immunity against it. Armed with this knowledge, people could re-enter work spaces where the risk of COVID-19 exposure is high, and do so knowing that they are unlikely to contract and fall ill from the virus. He also explains the protocol he's developing to this end, which includes COVID-19 surveillance of individuals who are at risk but currently unaffected by the virus, testing of individuals who are showing symptoms, and testing of people who have recovered from the virus. Knight dives deep into the fascinating details of this work and the continuously evolving field of microbiome research. He offers listeners with an impressive amount of information on microorganisms, the latest research on virus-host microbiome mechanisms based on animal models, how bacterial and viral infections respond to certain dietary interventions, how microbiome analysis can be predictive for the development of certain diseases, and more. To learn more, check out the following resources: https://cmi.ucsd.edu/ http://humanfoodproject.com/americangut/ https://scholar.google.com/citations?hl=en&user=_e3QL94AAAAJ https://knightlab.ucsd.edu/wordpress/

Oliver Ryder, Kleberg Endowed Director of Conservation Genetics at San Diego Zoo Global joins the podcast to discuss the Frozen Zoo, the world's largest, most diverse, most characterized, and most utilized collection of its kind. Press play to discover the following: Why now is a time when more genetic samples can be collected than ever (and the importance of doing so as a result of loss of species and decline in numbers) How many institutions are sending samples to the San Diego Zoo for collection, and how many cells of individual vertebrates are already frozen in this genetic bank What type of useful and unprecedented knowledge the Frozen Zoo will bring about regarding molecular genetics and stem cells Only within the last 60 years or so has it been possible to grow animal cells in the lab, freeze them, and revive them in a way that allows them to resume their function. This technology has made a huge contribution to the field of genomics and conservation science, allowing for a better understanding of the evolution of life, errors in the transmission of chromosomes that cause disease, extinction risks of certain species, and genetic diseases in endangered species to provide better health care and prevent extinction. The Frozen Zoo in San Diego was founded by physician Kurt Benirschke with the goal of helping to conserve endangered species. It now contains cells of 10,000 individual vertebrates (fishes, reptiles, amphibians, birds, mammals) and 1,200 species. This, however, is just the tip of the iceberg; the goal is to continue adding to this collection until samples of all 60,000-70,000 vertebrate species have been obtained. Ryder discusses many fascinating topics, including the collection of several high priority species samples, the increasing need to integrate efforts to save species in natural habitats that are preserved in human care, how scientists can access the database of frozen genetic samples, the Vertebrate Genome Project, how the genetic sequencing of animal genomes can provide interesting insight into human disease assessment, the ethical aspects of this type of work, and more. For more information, visit institute.sandiegozoo.org.

Professor of neurology at the UCSF Weill Institute for Neurosciences, Ying-Hui Fu, joins the show to discuss human sleep behavior. On this episode, you'll learn the following: How genetics could hold the key to understanding how some people not only survive, but thrive off of just a few hours of sleep per night (and how an understanding of the molecular mechanism at play could allow us all to have more efficient sleep) How genes play an important role in human sleep behavior Whether or not it's actually "better" to be early to bed and early to rise, rather than late to bed and late to rise Ying-Hui Fu, PhD, discusses the focus of the research being conducted in her lab at the Weill Institute for Neurosciences in San Francisco, CA. Her work centers on two areas: the circadian rhythm, and sleep duration. For well over two decades now, Fu has studied and conducted research in this field and found that genetics and genomics play an important role in determining sleep behavior, including whether a person is a so-called night owl or early bird, and how many hours of sleep per night a person needs in order to achieve optimal health and function. "I'm most interested in understanding…how to regulate sleep efficiency, because if we can increase it for everyone, then the incidences of all kinds of disease will drop significantly…and to me that's much better than trying to find cures for one disease at a time," says Fu. She continues by explaining the importance of understanding and harnessing the power of sleep efficiency in modern society through an examination of the relationship between genetic information and sleep regulation. Fu discusses a number of interesting topics, including the way in which the benefits of therapies and medicine can be maximized through administration at times that correlate with certain times during an individual's circadian rhythm, the increasing demand for shift workers and how detrimental night shift work can be for those who are early risers, the way in which sleep schedules change throughout different stages of life (e.g. teenage years versus old age), how a set of molecular reactions related to signals integral to the circadian rhythm regulates more than half of the genes in our bodies, how to measure sleep efficiency, and so much more. Tune in and check out http://scienceofsleep.org/ and http://neugenes.org/ for more.

Sean Gibbons, PhD, is a distinguished investigator at the Washington Research Foundation and assistant professor at the Institute for Systems Biology. He joins the show today to discuss the work being done in his lab. Tune in to learn the following: How species diversity in the human gut microbiome may lend itself to health and disease states of the host, patterns seen at the high and low ends of diversity, and how to qualify the meaning of "diversity" What findings Gibbons' work has shown, including the importance and implications of the intimate connection between the metabolites produced in the gut and the metabolites circulating in the bloodstream What patterns and characteristics are found in the microbiome during aging, and how analysis in this regard could provide predictive information about mortality Gibbons has a background and long-standing interest in the ecology, microbiology, and evolutionary biology of microbial communities, and for the past several years, he's been studying the human body through this lens. His lab is focused on trying to understand the variation in the ecology and evolutionary dynamics of the microbial communities that drive changes in the molecular phenotypes of host organisms. Gibbons and his team are accomplishing this by looking at the microbiome of healthy and sick individuals, as well as detailed molecular phenotypic data on the metabolome, proteome, human genome sequence, and dietary and lifestyle measurements. The ultimate goal is to understand what amount of variation in the ecology of microbial communities in the human body is coherent with variation in disease states. By doing this, the hope is to determine where the microbiome is involved in the etiology of disease. Gibbons discusses a number of fascinating topics, including the significance of low versus high species diversity in the gut microbiome, how bacteria in the gut compete and interact with one another, patterns found in the relationship between ageing and the gut microbiome, how information about the structure of someone's microbiome can be obtained by analyzing the metabolites in a sample of their blood, why a reliance on mouse models in the study of the human microbiome is not ideal, how Gibbons' team is trying to develop methods that will bring research findings closer to showing causality as opposed to just correlation, the importance of longitudinal data and interventional studies for moving the microbiome into clinical medicine, and so much more. Check out https://gibbons.isbscience.org/ to learn more.

Dr. Vinicio de Jesus Perez is an associate professor of pulmonary and critical care medicine at Stanford University, and practicing cardiopulmonologist who specializes in research and the clinical care of patients with pulmonary hypertension. He joins the show today to discuss the details of this interesting and important career, including the following: What the difference is between systemic hypertension and pulmonary hypertension How pulmonary hypertension has emerged as an increasingly common and complex disease since the 1960s, and what signs and symptoms patients generally present with What drugs and interventions can be used to treat different forms of pulmonary hypertension, and the importance of educating and supporting medical professionals in this area Dr. De Jesus Perez begins by illustrating the road that led him to pursue a path of medicine in the field of cardiopulmonology and critical care. He details one of the most difficult and memorable patients he saw in his early days as a medical intern, and how the experience spurred his desire to dive more deeply into an understanding of pulmonary hypertension. He explains the fascinating and somewhat unusual uptick in the number of cases of pulmonary hypertension in the 1960s in correlation with a weight loss drug called aminorex, and the discovery that pulmonary hypertension can be both a disease on its own as well as a complication of other disease processes, including lung fibrosis, left heart failure, kidney failure, HIV, and scleroderma. In order to meet the needs of patients with pulmonary hypertension and properly equip medical professionals for dealing with the disease, Dr. De Jesus Perez's group was one of the first to establish a pulmonary fellowship program aimed at training professionals to understand, diagnose, and treat pulmonary hypertension. Tune in to hear the full conversation and learn about the many resources for additional information on pulmonary hypertension, including http://med.stanford.edu/wallcenter.html.

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.

Curtis Suttle, Professor, Institute for the Oceans and Fisheries, The University of British Columbia, provides an overview of his work studying viruses that live in the oceans as he explains the ecological importance of viruses and much more. Podcast Points: Just how important are viruses to population and change? What viruses do to exist and fulfill their missions How do viruses infect cells? Suttle talks about his background, and how his early years as a sailing enthusiast opened his mind to the possibilities of learning more about the oceans. Upon discovering research vessels on his early voyages, he was intrigued about their missions. He discusses his PhD work and some of those he worked with who were already studying bacteria. As Suttle explains, bacteria are important, critical actually, to the balance of the oceans. And in fact, more than 95% of the living material in the oceans, by weight, is microscopic. To put this in perspective, these microbes produce about one-half of the oxygen on the planet. Continuing, the PhD discusses his work investigating ecology and viruses, moving into his later studies and experiments studying viruses that might infect phytoplankton. Additionally, Suttle shares the interesting stories from his childhood, as he and his family circumnavigated the globe on their small sailboat. He discusses his journey and the people they met, and how they were able to survive and provide for themselves, etc. Getting back to his remarks on viruses, Suttle explains the paradigm shift that has occurred, in terms of what we know about the ocean's microorganisms. Cycles are quick and the implications are large, and ultimately it is the microbes that are driving much of the change. Suttle explains how viruses have an important role of maintaining balance within a species, and when there is an overabundance, viruses advance and effectively control the expansion of species. Suttle explains how viruses are incredibly diverse and how they can encode complex genetic information in regard to DNA and RNA. Suttle talks about his early grant proposals for viral discovery, and how he came to study certain areas within his field. He expounds upon the overwhelming number of viruses that exist all over the world, and how they even exist above us, in the atmosphere.

Computational biologist Dr. Reyes discusses the basics of bacteriophages (viruses that infect bacteria) and bacteria interactions as well as current research. He covers How the majority of viruses and bacteria interactions are mutually beneficial, in what way, and why; What makes a phage move on to other bacteria, what it takes with it, and what effect that has; and How this particular strain of coronavirus is an RNA virus, what that tells us about how it works, and what it may take to get a vaccine. Alejandro Reyes Muñoz is an assistant professor in the Department of Biological Sciences at La Universidad de Los Andes in Bogotá, Colombia. He has investigated the importance of gut health and the interactions of microbes in the gut. In this podcast, he discusses phage-host interactions. He explains to listeners that it is important to consider the biodiversity of all the different environments that exist for bacteria, including the human gut. He explains why the question "what is a virus/host interaction like" is a very complex one. He adds that there are many different ways in which a virus and host need to interact to get to the point of a successful infection. Furthermore, he comments that the worst thing a pathogen can do to itself is to kill a host quickly. He describes more about this complicated and active relationship that has created a city-like architecture of microbes in the human gut, elucidating the importance of gut health. He also explains how genetic material is exchanged between the two and why each gains various benefits and what they are. He also addresses the coronavirus strain we currently are facing and discusses what scientist have observed about its mutation rate as well as the type of virus it is and what that implies about its behavior. Reyes also tells listeners about the complexity of understanding genomes and while scientists may sequence a virus genome, they can't predict what about 70% of that genome codes for. Finally, he describes his current work as developing computational methods to id some of the genes that those phages are coding for. For more information about the coronavirus sequencing, he directs listeners to a phylogenetic tree available at https://nextstr ain.org/ncov/global For more about the work of Alejandro Reyes Muñoz, see his lab website at https://bcem.uniandes.edu.co/bcem-lab/areyes.html

The founder of The Quantum Computing Report, Doug Finke offers listeners a perfect distillation of the basics of quantum computing alongside the latest advances. He describes The two twentieth century physics advancements quantum computing uses, namely entanglement and super-positioning and what they are, The challenges of quantum computing including the error rate, qubit de-coherence, and crosstalk alongside physical requirements such as the intense cooling, and Current quantum computing industry issues, including the lack of a shared computing language and the attempts to reach a "quantum advantage," a step that will bring quantum computing into the commercial field. Doug Finke has been involved in computing for over 30 years, following industry elements such as semi-conductors, the storage industry, and more. His research and reporting have helped drive the growth of quantum computing. In this podcast, he discusses the differences between classical computing and quantum technologies. First, he explains that our classic computers are based on the physics of the 1800s. He adds that in the 20th century, scientists like Einstein and Heisenberg came up with quantum mechanics—physics that involves entanglement (where two things are linked) and super positioning (can hold a mixture of 0 and 1 at same time). Classic computers of today don't take advantage of that phenomena, he explains, but quantum technologies and quantum computing do. He adds more about the probabilistic form of the answers derived from quantum computing, the need therefore for carefully crafted algorithms, and the accompanying issues of error rates and why. Along the way, he describes the special nature of a qubit and how it holds all of these technologies. He finishes by addressing current industry directions, the possibility of quantum computing commercialization, and what type of access the average user may have. For more see the website, https://quantumcomputingreport.com/, where you can sign up for his weekly newsletter that summarizes quantum news with applicable links.

Michael Snyder, PhD, is a Stanford W. Ascherman Professor and Chair of the Department of Genetics at Stanford, and Director of the Stanford Center for Genomics and Personalized Medicine. By tuning in, you'll learn the following: How your smartphone can be converted to your own personal health dashboard, allowing you to effectively manage and monitor your health How continuous glucose monitoring can help people manage diabetes or detect pre-diabetes, as well as determine which types of foods cause glucose spikes (different people experience glucose spikes in response to different foods) What the number one stumbling block is to rolling out various types of technology that can quite literally save lives by identifying illness early on, rather than after it's too late "To be quite frank, I think the way we practice health care these days is entirely wrong…that is to say we typically focus on people when they're ill and we really don't spend much energy trying to keep people healthy…I want to transform that…and actually catch disease at its earliest time so we can really work on health care and not sick care," says Dr. Snyder. According to Dr. Snyder, the key is in following people while they're healthy in order to establish a healthy baseline, and thereby detect signs of illness earlier on—before a disease or illness progresses. He says that advanced technologies have the ability to provide people with an unprecedented amount of access to their personal health data, and with little to no effort on their part. The research in the Snyder Lab is focused on sequencing genomes to predict genetic risk for disease, and has shown promising results. Out of the first 70 people sequenced, they found that 12 had clinically actionable information in their genome, including a mutation that placed a patient at high risk for breast cancer, and a gene that predicted a heart defect in a young patient. Dr. Snyder and his team are also using omics technology (e.g. proteomics, metabolomics) to measure as many molecules as possible from a sample of blood in order to ascertain a more precise understanding of a person's health state. Dr. Snyder discusses the use of wearables that can detect changes in heart rate, temperature, blood oxygen levels, and other metrics in order to not only provide people with an understanding of their baseline measurements, but alert them to unexpected or out of place changes that may indicate disease. Press play for the full conversation and learn more about the work being done at Snyder Lab by visiting http://snyderlab.stanford.edu/.