Natural Prodcast

On this bonus episode of Natural Prodcast, it's the Self Promotion Episode! Dan chats with new-ish co host Jackie Winter, from the University of Utah, about her secondary metabolism research on weird microbes and bioactive compounds in the Great Salt Lake. Then, Dan talks (maybe way too much) about the Secondary Metabolism Collaboratory, or SMC, JGI's new data portal for natural product biosynthetic gene clusters.Episode transcript at jgi.doe.gov/natural-prodcast-episode-24-jackie-winter-and-smc.

Natural Prodcast talks to Aaron Puri, from the University of Utah's Chemistry Department. We talked about carbon-fixing methylotrophs, quorum sensing, and inverse stable isotopic labeling.

In this episode, Dan and Jackie talk to Alison Narayan, from the University of Michigan's Life Sciences Institute and Department of Chemistry. We talked broadly about the field of "biocatalysis", about her DNA synthesis project with the JGI to explore flavin monooxygenases, and what we all need to do in the future to figure out how to make predictions about the functionality and chemical capabilities of enzymes. Also, the Prodcast formally declares its position on candy corn. 

Natural Prodcast's interview with Elizabeth (Betsy) Parkinson, from Purdue, about bacterial signaling molecules and regulation of biosynthetic pathways, semisynthetic cyclic peptides, student mental health, and getting kids interested in microbiology. 

Natural Prodcast's interview with Vanderbilt Professor of Chemistry, Brian O Bachmann. 

Natural Prodcast talks to Prof William Fenical of Scripps Institution of Oceanography in San Diego about the beginnings of marine natural products, his experiences in drug discovery, and exploring marine bacteria. 

It's a crossover episode! Menaka Wilhelm, from JGI's Genome Insider, and I talk about how to work with the JGI, specifically in the form of the Community Science Program, or CSP. We talked to Deputy of User Programs, Tanja Woyke and Project Manager Miranda Harmon-Smith about all the details of what makes a good CSP, how to apply for one, and what happens once it starts. 

Natural Prodcast's Dan and Alison talk to Dr Cassandra Quave of Emory University, and author of The Plant Hunter

Natural Prodcast presents our interview with Professor Marcy Balunas, currently at the University of Connecticut's Department of Pharmaceutical Sciences but soon moving to the University of Michigan's Department of Microbiology and Immunology. In this episode, we discuss her work in in many areas of chemical exploration of natural products for bioactive compound discovery, understanding symbiosis, and a JGI project around ants and their fungus farms.

This is Natural Prodcast's conversation with Professor Katherine Duncan from the University of Strathclyde in Glasgow, Scotland. Dr Duncan's work focuses on marine microbial chemical ecology. We also discuss Actinobase, molecular networking, and the future of integrated secondary metabolism data.

Our guest on this episode is Dr Nigel Mouncey, JGI's Director, and also lead of the JGI's Secondary Metabolites Science Program. Since his arrival in 2017, Nigel has led a vision for the JGI that sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users. Nigel has a long scientific background in pathway and gene regulation, and a distinguished career in industry developing natural products for commercial use.

In this episode of the podcast, we talked a lot about terminology, especially around "secondary metabolism" versus "specialized metabolism" and "primary metabolism" versus "centralized metabolism" and why and how they're different when we take things from a human-centric view rather than a microbe-centric one. It was so fun, and I learned a ton. I hope you will too!

This is our interview with Nadine Ziermert, from the University of Tubingen. This continues our short series of genome mining, the science of examining DNA sequence to try and predict the structures of secondary metabolites and to understand their evolution. It was a fun, wide-ranging conversation, where we talked about our shared experience working with the marine bacteria Salinispora at Scripps Institution of Oceanography, her accidental entry into data analysis, the evolution of secondary metabolite pathways as viewed through metagenome studies, and what more JGI and others can do to enable progress in this area of natural products.

In this episode, Alison and I talk to Marnix Medema, from Wageningen University in the Netherlands. Marnix and his collaborators have a fantastic set of software tools for exploring secondary metabolite biosynthetic gene clusters (BGCs). Most people in the field are going to be familiar with AntiSMASH, which is available for analysis of your genomes on the web, or you can download a docker container or Anaconda/bioconda package or the source code and run it yourself on your own computer. MIBiG is a repository of experimentally characterized and manually annotated BGCs. And now BiG-SCAPE and/or BiG-SLICE can compare your gene clusters and group them into families, which you can also look at in BiG-FAM. This ecosystem for secondary metabolism has become transformative to the natural products community, and Marnix's enthusiasm for science and excitement about creating fantastic collaborative research projects is infectious. This episode should make a nice jumping-off point into the deeper end of genome mining after the Genome Mining Primer episode, last time.

This is one of our "Primer" episodes, in which Alison and Dan discuss the science of genome mining. We talk about the California Gold Rush (it's relevant! I promise!), talk about how genome sequencing has changed genome mining over the years, and we talk about a new publication out of JGI in which Dan conducted genome mining on metagenome-derived genomes. Check out http://naturalprodcast.com for show notes with links to papers and other learning resources.

This episode features our conversation with Roger Linington, from Simon Fraser University. Roger is a natural products chemist, and his research group works in metabolomics, drug discovery and screening, structure elucidation, and chemical biology. In recent years, his group has turned to some software development in order to build the tools that they need, and The Natural Product Atlas, a high-quality freely-available natural products structure database is one great result. In our conversation, we talk about NPAtlas, and the large international collaboration that produced it, what one can do with all that information, and we muse on how to start connecting the large and ever-growing set of omics data that natural products research continues to produce.

This is our conversation with Eric Schmidt from the University of Utah. We talk about marine natural products from cone snails, sponges, tunicates, and about the chemistry of RiPPs.

Our conversation with Ben Shen, from The Scripps Research Institute (TSRI) in Jupiter, Florida. Ben and Alison and I talk about enediynes and their use in medicine, how Ben got fascinated with natural products working on terpene chemistry, TSRI's acquisition of the Pfizer strain collection, and our collaborations to sequence that collection, mine genomes, and develop new technology to access natural products. As always, check out the show notes and get transcripts for all of our episodes at http://naturalprodcast.com

This is a conversation with Marc Chevrette. Marc is a post-doc in Jo Handelsman’s group at the University of Wisconsin, where, among lots of other things, he works on the Tiny Earth project, which you’ll hear him describe. He’s also a really good friend of mine. I met him when we worked together at the late great Warp Drive Bio, a biotech startup where we did genome mining together. Marc was the Head of Experimental Genomics there, before he decided to leave for graduate school and pursue his PhD.

This is the second of our conversations recorded at the SIMB Natural Products conference, which took place last January 2020 in San Diego. San Diego, of course is the “home turf” of my post-doctoral mentor, Brad Moore, who has join appointments at UC San Diego and Scripps Institution of Oceanography. Alison and I were lucky to get some time to sit down and have a great chat with him. I kind of lost count of how many times Brad used the words “fun” and “magical” when describing his science, which is kind of the hallmark or the philosophy of his group and I think in hearing him talk about natural products you’ll get a good sense of what it’s like working with him. We talk about his father, the legendary marine natural products chemist, Richard Moore, and get into seaweed, robots, algae, and biocatalysis — and he makes fun of me a lot, though I actually edited most of that out.

This episode is our conversation with Nancy Keller, a fantastic fungal natural products researcher from the University of Wisconsin. Like we discussed in the primer podcasts, which you should be able to find earlier in the feed, the secondary metabolism field has been dominated for … well, as long as I can remember, by bacterial research. So it was great to hear her passion and enthusiasm for fungi. And we talk a lot about some of the technical challenges to that, most of which seem to be history.

This is Dan again, and you’re about to listen to the 3rd and final part of Natural Prodcast’s “Primer” episodes. This IS the third part, so if this is the first episode you’re checking out, you probably want to go back and listen to the first two parts so you understand what’s happened so far in the conversation between me and Alison. In the previous episodes we talked about the basic science and the history of the field of natural products or secondary metabolism, depending on which term you prefer. In this episode we’re going to finish up by talking about the modern, post-golden age history of natural products discovery, and we’ll talk a lot about the current state of things, and what we’re hoping to accomplish at JGI in this area.Like I said in the intro to the first episode, after this we’re going to be spending some time talking some great scientists, who all have really interesting stories and very cool research. I hope you’ll stick around. But, for now, here’s episode 3 of the Primer!

This is part 2 of our “primer” episode, so if you ended up here somehow without having listened to the first part, you might be a little lost, and I’d suggest you go back and check the first episode out. This one continues the introductory conversation between myself and Alison, and we continue with the basic ideas of the science of natural products, and we dive into the very early history of the field. If you continue on, in the next episode you’ll hear us talk about the modern history of natural products and the state of the field today.

These first three episodes were recorded as a longer conversation, which I cut into more digestable pieces. In the first episode you’ll meet me, and my co-host, Alison. We’ll tell you some stories about natural products, so you can get a feel for why I think this is so important, and we’ll start to explain some of the terms and the basics so that you, the audience, who might not be familiar, can start to understand what this is all about. In the second episode, we’ll talk some more about the differences between primary metabolism and secondary metabolism, and we talk about the early history of the field. Then, in the third episode, if you’re still with us, we’ll discuss the modern history of natural products and where we are today. After that, we have lots of great conversations that we’ve already recorded with some excellent scientists, and that’s probably how we’ll continue for a while. To be fair, it’s probably going to help you some to have some basic knowledge of modern biology. We’re trying to keep this as general as possible, but scientists love technical jargon. If you don’t have that background, well, everybody starts somewhere right? Most of what you need to know is a Google search away!

HI, I’m Dan Udwary. I’m a chemist, and I do research to try to understand natural products, and how living organisms do the amazing chemistry that makes life diverse and unique. I’ve been a professor, I’ve worked in the biotech industry, and now I work at the Department of Energy Joint Genome Institute. I love my work, I love this field, and I’ve met a ton of super cool scientists along the way. Now, I want to tell you about them.So, join me and my co-host, Alison Takemura. She’s my colleague at JGI, and she’s going to learn about natural products, maybe along with you! We’ll chat about the science.And we’ll talk to some of the most amazing scientists I know, about what they do.So, check it out. Natural Prodcast. Coming soon, on Apple, Google, Spotify, and wherever you get your podcasts.