Dr. Justin Siegel begins this episode by explaining what enzymes are, how they have evolved, and why Dr. Siegel is motivated to try to engineer enzymes to perform functions tailored to help humanity instead of to perform functions based on how they evolved in nature. He explains the primary goal of the work discussed and relating enzyme sequence to function. Dr. Siegel also explains how his work was the first of its kind by scaling up enzyme design to hundreds of mutants instead of...

Dr. Justin Siegel explains the past, present, and future of wet lab work and wet lab automation. We start by hearing a description of what it is like to work in a wet lab, covering the contrast between the excitement of seeing life changing results and the countless hours of monotony that is often involved to produce these results.  We then begin discussing where automation will fit in to help alleviate the burden of long term monotonous work in the wet lab. We learn about the challenges of...

Dr. Afshin Beheshti begins this episode by explaining what microRNAs are and why they are emerging as an important area of biological research. He then explains how microRNAs relate to viruses, which is a recently developing area of research in this already young field of study. Dr. Beheshti then tells the story of how he started to discover that microRNAs could be a driver of COVID-19 infections.  His story begins by using microRNA analysis tools to analyze COVID-19 infected patients from...

This episode concludes the podcast’s series of episodes focused on space biology and space omics. NASA scientist Dr. Afshin Beheshti discusses the many high level hazards and corresponding molecular features of spaceflight throughout this episode. For instance, we begin with a discussion of the hazards of radiation and microgravity. Dr. Beheshti spends time explaining a high level view of what each hazard is, why it is a concern for spaceflight, and educates us on many useful and interesting...

This episode discusses Dr. Tejaswini Mishra’s recent publication in Nature Biomedical Engineering: https://www.nature.com/articles/s41551-020-00640-6 Dr. Mishra begins the episode by explaining the origin story of this work and how the idea for this paper came to be. She then explains how this study enrolled thousands of participants and used the participants’ smartwatch or wearable device data to detect COVID-19 infections.  After explaining how this study began, Dr. Mishra discusses how she...

This episode continues our series of episodes on space biology and #SpaceOmics with Dr. Tejaswini Mishra. Dr. Mishra introduces The NASA Twins Study, a cornerstone scientific work where two twin astronauts were monitored, with one twin traveling to space, and one staying on earth. Dr. Mishra explains the importance of studying long term spaceflight missions, how The NASA Twins Study was set up in a particularly great way to study spaceflight impact, the many different types of data collected...

For people who work in the life sciences, a very common occurrence is for folks who work on the "wet" side of research, largely doing bench work, to become interested in or start wanting to transition to doing more "dry" research, like computational research in bioinformatics. In this special episode, dedicated to those thinking about transitioning from "wet" lab work to doing more "dry" lab type work, my guest Dr. Willian da Silveira explains his own transition from a full bench scientist to...

In this episode we begin discussing the biology of spaceflight with Dr. Willian da Silveira. We start by hearing the story of how Dr. da Silveira's recent high profile space omics paper (https://www.cell.com/cell/pdf/S0092-8674(20)31461-6.pdf) came to be. He first describes the NASA GeneLab and how he got involved, and how his story of this paper began with an analysis of some liver transcriptomics data. We hear about all the different types of data used in this study, including epigenetics...

Dr. Hayden Metsky begins by introducing the ADAPT method for doing large-scale detection of viruses. ADAPT is a computational method that aids the design of CRISPR-based viral testing. He then discusses the motivation for ADAPT and how it relates to his previous works like CATCH. In comparing ADAPT to other work, Dr. Metsky discusses, for instance, differences between CRISPR-based testing and more traditional testing like qPCR. In discussing the challenges of designing diagnostic tests and...

Dr. Hayden Metsky begins the episode by describing his goal of being able to harness sequenced viral genomes to computationally design diagnostics, therapies, and vaccines. He discusses the value of having methods available that can handle all available genomic data for diverse species for diagnostics and therapies. Next, we learn how CRISPR can be used in a diagnostics setting. Dr. Metsky explains how collateral cleavage broadens the use of CRISPR beyond simply being a tool for genome...

In this episode we focus on the applications side of synthetic biology for the environmental sciences and environmental microbiology with Dr. Ilenne Del Valle and Emm Fulk. To start, we walk through the more classical omics approaches for understanding environmental microbiology, setting us up for newer synthetic biology approaches. We then discuss the main questions in environmental microbiology that synbio is well suited to help answer. We discuss a few specific problems such as quorum...

Dr. Ilenne Del Valle and Emm Fulk introduce the topic of synthetic biology in this episode. I start by asking, "What is synthetic biology?" We then begin digging into some of the intricacies of synthetic biology by learning about biosensors; biosensors are a fundamental component of synthetic biology for translating environmental inputs and outputs. We next talk about all the different molecules that biosensors can sense that we could use for various applications.  Our conversation continues...

Dr. Kyle Frischkorn explains the interplay between different sample analysis methods such as transcriptomics and proteomics. He starts by explaining some of the basics of both transcriptomics and proteomics and gives a refresher on the central dogma. This explanation covers aspects of these methods such as a high level description of what they are, how they work, and what data you get from them. He also mentions more detailed considerations such as difficulties with mapping RNA back to...

In this episode, we attempt to take a look behind the machine of science with Nature Communications senior editor Dr. Kyle Frischkorn. We begin by simply asking the question, "How do you publish in Nature?" Dr. Frischkorn breaks down several of the main hurdles to getting published in Nature. These include having striking findings in the actual research and picking the right venue from within the Nature portfolio. We learn about different aspects that could potentially help or hurt your...

Dr. Leor Weinberger begins this episode by talking about his motivation for developing a novel therapy for HIV. He explains the fundamental mismatch between the mutation and transmission of the disease and how our therapies work, which inspired him to take a novel approach to try and combat the disease.  We discuss topics such as the potential for scientists to give up on an HIV vaccine and why it seems like there are no good general antiviral drugs. To lead up to discussing Dr. Weinberger's...

This episode begins by asking the question, "Why is it that we don't have an HIV vaccine after 40 years, but we do have a COVID-19 vaccine after one year?" Dr. Leor Weinberger explains that the answer to this question is primarily due to the existence (or lack thereof) of natural convalescents and whether the immune system is able to beat the virus. Dr. Weinberger further explains that there have only been two "recovered" people who had HIV. These two recoveries happened through bone marrow...

In this episode, Dr. Sabrina Green discusses the clinical aspects of phage use. We start by going back to one of the first ever uses of phage for a bacterial infection before discussing how phages are used now. Dr. Green explains a wide range of details related to clinical phage use. Topics discussed include cases today where phages are used, the safety of phages for clinical use, regulatory considerations for phage therapies, the pros and cons of phages, how specific phages are matched to...

Dr. Sabrina Green introduces the concepts of phages and phage therapy. She describes what phages are and gives us a bit of history on phage therapy, describing reasons why antibiotics were widely adopted despite phages being discovered first. She also discusses why phages have become so important in the light of emerging antibiotic resistant pathogens. Dr. Green explains the mechanisms of how phages work and how these mechanisms lend themselves well to, for instance, scaling to different...

Dr. Zahi Fayad and Dr. Robert Hirten return to continue their discussion on wearable technology. This episode revolves around the study Dr. Fayad and Dr. Hirten performed to find out if wearable devices can identify and predict COVID-19. They discuss some of the struggles they had being “largely restricted in the data they could collect”. Their findings have the potential to be ground-breaking and showed “there are significant changes in your heart rate variability over 24 hours, which allows...

Dr. Zahi Fayad and Dr. Robert Hirten discuss all things wearable technology. Throughout the episode we learn about the exciting potential of this technology for conducting health studies and for the general wellbeing of the population. Dr. Fayad and Dr. Hirten explain what wearables do for athletes and for the general health of the public, even predicting “there is a market for the future for scaling it up and making it bespoke”. Dr. Fayad explains why he utilises many different wearables all...

In this second part of our history of metagenomics with Matthew Schechter, we start with a description of what a metagenome contains and how you analyze this type of data. Matt explains a few high level concepts such as metagenome assembly, metagenomic assembled genomes, contigs, contig binning, and genome completeness. Matt explains how metagenomics can help answer previously unanswered questions and even generate new hypotheses like in the example of the Candidate Phyla Radiation. Matt...

In this episode we begin our history of metagenomics with Matthew Schechter. Beginning with highlights like the initial ability to see microbes with a microscope and growing microbial colonies, we work our way through the history of metagenomics leading to modern day sequencing. Matt describes a discrepancy between culturing and what is present in a sample, and how sequencing began to overcome this discrepancy. Matt covers what 16S sequencing is and where it fits in the history of...

Dr. Heer Mehta starts by going over several of the ways that bacteria become resistant to antibiotics. Dr. Mehta explains the connection between specific antibiotics and specific drugs, and how she uses this information to know what to look for when studying the outcomes of experimental evolution studies. She explains how her group can isolate individual mutations that arise as a pathogen becomes resistant, and determine the difference in the protein structure caused by the mutation. We then...

Dr. Heer Mehta first goes over some basics of what antibiotic resistance is, why it is a global concern, and some related history. Dr. Mehta explains how bacteria are able to evolve to become resistant to antibiotics. She goes on further to explain how experimental evolution is one way scientists can understand this process and potentially use as a weapon in humanity’s battle against antibiotic resistant pathogens. She explains additional tools we can use such as microscopy and genome...