144 - micro binfie Pathoplexus part 1

Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://pathoplexus.org/about/eb * Dr. Theo Sanderson - https://pathoplexus.org/about/development-team * Mr. Arthur Shem Kasambula - https://pathoplexus.org/about/development-team

143 - where we catch up on our professional lives by Microbial Bioinformatics

The crew talks about the genomeqc ecosystem. Check it out at https://happykhan.github.io/qualibact/ Errata: The project name was chaned to qualibact and is no longer genomeqc as mentioned on the episode.

In this episode of the Podcast, hosts Lee Katz and Andrew Page delve into the intricacies of clinical metagenomics. Joined by experts Torsten Seemann and Finlay Maguire, they explore the challenges and methodologies involved in identifying pathogens in clinical samples when traditional diagnostic methods fail. They discuss the types of samples analyzed, the impact of low DNA concentrations, and the complexities of sequencing data interpretation. The conversation highlights the importance of interdisciplinary collaboration between bioinformaticians and clinicians in managing difficult infections. Despite the hurdles, clinical metagenomics is presented as a complementary tool aiding in diagnosis, emphasizing the need for genomic literacy among healthcare professionals.

On this episode we are joined by Sara Zufan to discuss her PhD journey and recent projects. The episode covers various research experiences and challenges in the field, including the rapid detection of AMR using nanopore sequencing, COVID-19 projects, hepatitis A outbreak investigations, and Lassa virus surveillance in Liberia. The guests share insights into their professional journeys, their experiences working across different continents, and the future of microbial bioinformatics research.

In this episode of the Micro Binfie Podcast, host Andrew Page takes listeners to the heart of the microbial genomics hackathon in Bethesda, Maryland, for an engaging conversation with special guest Megan Phillips, a PhD student from Emory University. Megan delves into her research on Staphylococcus aureus (MRSA), highlighting its fascinating dual nature as both a harmless and potentially serious pathogen. Megan discusses the complexities of tetracycline resistance, particularly focusing on plasmid-mediated mechanisms involving the pt181 plasmid. She explains how this plasmid’s efflux pump, encoded by the gene tetK, contributes to variable resistance levels and the factors influencing MIC (Minimum Inhibitory Concentration) variability. Listeners will learn about the intricacies of plasmid copy numbers, their global spread across clonal complexes, and the occurrence of horizontal and vertical gene transfer. Throughout the episode, Megan shares insights on working with short-read sequencing data and the strategies she employs to detect plasmid presence using tools like BLAST. She also touches on the challenges and fascinating discoveries of tracking historical sample data and integrating findings from older research papers, showcasing her appreciation for the poetic style of scientific writing from the 1940s. For those interested in antimicrobial resistance, evolutionary microbiology, and the subtleties of bacterial genome analysis, this episode offers a compelling blend of technical details and engaging storytelling. Tune in to hear more about Megan’s upcoming publications, her experiences navigating complex genomic data, and her thoughts on antimicrobial stewardship and historical perspectives on drug resistance.

In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up the virus's spread and the response to it, and that decisions about managing a crisis are based on societal values, not just science. In part one, the hosts discuss the movie's depiction of the R0 value. They note that while this explanation is useful for the audience, it is unlikely that an epidemiologist would need to explain this concept to other epidemiologists. The group notes that the MEV1 virus is modeled on the real-life Nipah virus and comment on a scene where the genome of the virus is described as being 15 to 19 kilobases in length with 6 to 10 genes. They also discuss the movie's depiction of virus isolation and the unrealistic speed with which the initial assessment of the virus occurs. The podcasters touch upon the BSL4 lab and how the film depicts how the scientists behave. They also discuss the character of Matt Damon, who is exposed to the virus but does not get sick, and is an example of an asymptomatic carrier. In part two, the bioinformaticians examine the "genome dashboard" scene, noting the software's informative interface, which includes an alignment panel, protein structure, and a recombination map. They also discuss a scene where a phylogenetic tree is used to determine a change in the R0 value. They find this unrealistic because the tree is just a picture that doesn't accurately represent how a virus spreads. The group discusses how the bioinformatician is depicted in the film as moving in and out of the lab, which may have been realistic in 2011 but is less so in the present day. They discuss how the CDC is portrayed in the film, noting scenes that were filmed at the actual CDC, as well as their experiences at the CDC. The podcasters note the movie is very US-centric and that many international partners would be involved in solving a global pandemic.

In this episode of the Micro Binfie podcast, host Andrew Page is joined by Nikhita Puthuveetil, Senior Bioinformatician at the American Type Culture Collection (ATCC). They delve into ATCC's ambitious project of sequencing a vast array of organisms from their renowned collection, tackling the challenges of assembling complex genomes from bacteria, viruses, fungi, and more. Discover how Nikhita and her team navigate through genomic roadblocks, leverage cutting-edge sequencing technologies, and work to ensure accurate data provenance. Whether it's large viral genomes or evolving taxonomy, this episode offers a deep dive into the fascinating world of microbial bioinformatics and genomic curation.

Andrew, Lee, Torsten, and Fin muse over the future of MLST, Illumina, and Nanopore at the ASM NGS Hackathon

In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up the virus's spread and the response to it, and that decisions about managing a crisis are based on societal values, not just science. In part one, the hosts discuss the movie's depiction of the R0 value. They note that while this explanation is useful for the audience, it is unlikely that an epidemiologist would need to explain this concept to other epidemiologists. The group notes that the MEV1 virus is modeled on the real-life Nipah virus and comment on a scene where the genome of the virus is described as being 15 to 19 kilobases in length with 6 to 10 genes. They also discuss the movie's depiction of virus isolation and the unrealistic speed with which the initial assessment of the virus occurs. The podcasters touch upon the BSL4 lab and how the film depicts how the scientists behave. They also discuss the character of Matt Damon, who is exposed to the virus but does not get sick, and is an example of an asymptomatic carrier. In part two, the bioinformaticians examine the "genome dashboard" scene, noting the software's informative interface, which includes an alignment panel, protein structure, and a recombination map. They also discuss a scene where a phylogenetic tree is used to determine a change in the R0 value. They find this unrealistic because the tree is just a picture that doesn't accurately represent how a virus spreads. The group discusses how the bioinformatician is depicted in the film as moving in and out of the lab, which may have been realistic in 2011 but is less so in the present day. They discuss how the CDC is portrayed in the film, noting scenes that were filmed at the actual CDC, as well as their experiences at the CDC. The podcasters note the movie is very US-centric and that many international partners would be involved in solving a global pandemic.