Search

… advanced sequencing technologies to decode the genomes of microbes in their natural environments. This work … regulation, and noncoding RNAs in microbiomes. The insights from this work have the potential to drive innovations in … comprising the largest public collection of plasmid sequences identified from genomes, SAGs, MAGs, metagenomes …

… product reports on the evolution of genome mining and microbes with Mohammad Alanjary and Tilmann Weber to be a … there are any kind of dated references to the news, that’s why. But it was a really fun conversation. And I think … it would work, but we actually found fosmids. And we sequenced the whole fosmid at the time with Sanger …

… we have our conversation with Professor Alison Narayan, from the University of Michigan. I hope she’ll accept this … enzymes are, right? ALISON NARAYAN: Yes, and so that’s why I don’t like that sentence. I think that sometimes, we … association that might help? Like, if you have an unknown sequence or new flavin monooxygenases, you could say, oh …

Laboratory. Being a User Facility means that scientists from all over the world bring us big problems related to … stories about natural products, so you can get a feel for why I think they’re so important, and we’ll start to explain … was adjacent to what I worked on, but my experience of how microbes are interacting in the environment like, like my …

… genome mining on more than 50,000 genomes that we derived from meta-genome sequences. As always, you’ll find transcripts and show notes … for us– what organisms people use for genome mining, why it’s called genome mining, how the biosynthetic gene …

… at genomes and seeing where the really hard things to sequence were, and wondering what those … what those were … was looking to develop new methods for DNA sequencing of microbes. And what kept breaking our methods was these damn … functional was these secondary metabolite pathways. So why was that? What is it about secondary metabolite pathways …

And at the time, it was really exciting when people would sequence [DNA]. The genome was– well, that hadn’t really … polyketide synthase and then P3. We still don’t know why 20 years later. JACKIE WINTER: It’s pretty amazing, … them on a regular basis. So they are full of terrestrial microbes. So they’re open ecosystems. They’re not sealed off …

… use natural products necessarily. Fungi are large. They’re microbes, but they’re large microbes. And they have all … out introns and dealing with, you know, weirdness in the sequence. You know, some clusters are not clustered…   … it so easily with fungi. So…   NANCY: Yeah, I don’t know why. For example, with that – actually there’s a good talk …

… systems. No one was, at that time, really working with microbes from the ocean. So I felt there was a wonderful … then genomics happened. Dan: Yeah, I did my first genome sequence with you. Brad: That’s right,  Dan: JGI did it in … working with you, Dan, on this one, and we said, “Well, why don’t we have you know, the bioinformaticians go against …

… about the basics of genome mining, which is using DNA sequence to identify and interpret biosynthetic, secondary … biological perspective, like what was this bacterium, and why did your group want to study it? Marnix Medema: You mean … a nice example of going from a whole community with many microbes, hundreds of gene clusters, and then being able to …

… to identify over 27,000 microbial genes. The data from that study is now used across California State … of a course-based undergraduate resource experience. Hear from CSU San Marcos Professor Matt Escobar and UC Davis … of the JGI User Executive Committee, on how that study went from the lab to the classroom. …

This time, we’ve got a great interview with Ben Shen, from the Scripps Research Institute in Jupiter Florida. This … the paradigm of how to discover natural products. So, why I’m very excited to be working with Dan, you, with the … develop enabling technologies. ie how to translate the ATGC sequence into discrete small molecules. So, Dan, I’m very …