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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:
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:
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:
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:
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
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
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:
"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/.
Catherine Freije and Cameron Myhrvold are working on a test for the Covid-19 virus that will provide faster results than what's currently in use. They explain
Cameron Myhrvold is a postdoctoral fellow in the Sabeti Lab and Catherine Freije is a Ph.D. student in Harvard University's Program in Virology and is also working in the Sabeti Lab. These two virologists discuss an exciting step forward in rapid testing for the Covid-19 virus that involves CRISPR. First, they discuss some general concerns of understanding how long the virus may linger and when exactly we can know when someone is contagion-free. They explain that if we could test a lot of people more rapidly, it would be really helpful step forward.
They tell listeners that their test is quantitative and can let you distinguish between infection levels that are really low or moderate versus high. They then explain the mechanics of the virus test: basically, they use a CRISPR process called Sherlock that picks a target with Cas13 and amplifies it for inspection through the cleaving process and reporter signaling.
They explain that this general process has been used for other viral infections like the Zika virus and Dengue, but must be specified for Covid-19. They add that they are still in the optimization phase, getting the test to work as well as possible. However, the turnaround for use will likely be accelerated by the FDA. They address other concerns about testing for the virus and challenges they may face.
For more, see the lab website: https://www.sabetilab.org/
Dr. John Knight helped oversee a global competition to produce a more affordable dialysis system. He discusses
Dr. John Knight is a Professorial Fellow of the Renal and Metabolic Division and Professor of Medicine at UNSW Sydney and is Adjunct Professor of Pediatrics and Child health at their Children's Hospital. He was in private practice for several years focusing on pediatric chronic kidney disease. He recently joined a non-profit medical research group called The George Institute for Global Health in Sydney.
He describes their focus on questions about kidney treatment around the world including dialysis complications and chronic kidney disease: dialysis is highly successful but highly expensive. In most western countries, the community picks up the cost through taxes. The rest of the world can't afford that and many die from their kidney disease instead of receiving dialysis. Around 10 million world-wide need dialysis but only about 2.6 million are able to get it.
Knight describes the global competition called the Affordable Dialysis Prize, which The George Institute organized with the following terms: inventors should invent a low cost dialysis that uses solar power, is portable, can purify water from any source, and costs less than $1000 to manufacture. Dr. Knight tells listeners about the winner, about the group called Ellen Medical Devices Party, Ltd., he created to manufacture it, and describes the next phase of making it available worldwide to address dialysis complications and chronic kidney disease.
For more, see https://www.ellenmedical.com/, where viewers can sign up for a newsletter.
Debra and Miriam Aczel, wife and daughter of Amir D. Aczel, talk about goals of the foundation and what they've accomplished thus far. They tell listeners about
Debra G. Aczel, co-founder and co-director, and Miriam Aczel , co-director, talk about the Amir D. Aczel Foundation for Research. Miriam is also obtaining her PhD in London on environmental policy emphasizing global environmental change and climate science. In 2019, the Amir D. Aczel Foundation for Research held the "Symposium on the History of Mathematics: The Number Zero" in Phnom Penh, Cambodia. Debra and Miriam talk about the symposium as they explain how the foundation lives up to the spirit of what Amir wanted to bring about in the world. They touch on the story of Finding Zero, Amir's love for all things math, and how he believed telling a good story was a vital way to reach people about math and science.
His involvement with the k-127 artifact was substantial as he wrote about it as a key to understanding the zero symbol's origin in the region. The 2019 symposium prioritized this important history and Cambodian's place in the story. Miriam explains that the conference itself had two goals centered on sustainability: first, prioritizing the sustainability of relationships they were building between Cambodian mathematicians and world mathematicians; and second, substantiality through food and venue choices emphasizing global environmental change and climate science.
For more and to contact the foundation, see its web site at https://amiraczel.org/
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