Conversations with scientists

A conversation with David Neale, professor emeritus of the University of California Davis and director of the Whitebark Pine Ecosystem Foundation. As a forester and scientist, he works on trees, also the genomics of trees to understand more about their longevity and adaptability to events such as climate change. And he wants to empower the next generation people interested in these questions. (Art: J. Jackson, Music: Break of Dawn / Anthony Vega licensed from artlist.io.)

University of California San Diego researcher Dr. Gene Yeo is an athlete-scientist. He has completed two Iron Man competitions, a number of half Iron Man competitions and both full and half marathons. He says: "On these long long runs and long bike rides, you know, you get the time to sort of zone out a little bit, right. And it helps you focus on, you know, answering some questions." This podcast is about his approach to his sport, how it influences his science, what his sport gives him. And it's about his science, too, which is all about RNA. (Art: J. Jackson, Music Smoothy Moody by Mac A DeMia licensed from Artlist.io)

Cells push things around and get pushed around, it's all in a day's work. Tracking this, such as by tracking actin and the cytoskeleton, takes microscopy and labels. Lifeact, for example, is a popular, widely used label. This conversation is with the Lifeact developers Dr. Michael Sixt from Institute of Science and Technology Austria and Dr. Roland Wedlich-Söldner from the University of Münster in Germany. Among other topics, they talk about how the label came to be, how to use it, what's next and whether or not cells practice bodyslamming. (Art: J. Jackson, Music: Funky Energetic Intro by Winnie the Mook licensed from film music.io and Rice Crackers from Aves, licensed from Artlist.io.)

Dr. Steven Salzberg is a Johns Hopkins University researcher and director of the Center for Computational Biology at Hopkins. I spoke with him about genomics, about long-read sequencing, about human biology and human diversity, about funding, technology choice, about complete and incomplete genomes, about jobs in bioinformatics. He described his technology choices and about the choices one has to make in small labs. He shared his thoughts about the trend toward pangenomes and graph genomes. And he described how technology has changed and how happy that makes him. Teeny reminder, Steven Salzberg headed bioinformatics at TIGR, the Institute for Genomic Research run by J. Craig Venter. It was part of the venture to determine the sequence of the human genome. And yes, there were human genome assemblies based on teeny tiny read lengths. 

When scientists want to know about genes, chances are they use instruments called sequencers. Some of them can generate long-reads, which helps with analyzing genomes. The method of the year according to Nature Methods is: long read-sequencing. For a story I chatted with scientists at companies and in academia about long-read sequencing and did some podcasts, too. This episode is with Dr. Gordon Sanghera, CEO of Oxford Nanopore Technologies. (Art: J. Jackson).The following music was used for this media project: Winnie The Moog, Funky Energetic Intro and Acid Trumpet by Kevin MacLeod Free download: https://filmmusic.io/song/3340-acid-trumpet License (CC BY 4.0): https://filmmusic.io/standard-license

When scientists want to know about genes, chances are they use instruments called sequencers. There are quite a few companies that make sequencers. These instruments can give a read-out for example of a stretch of DNA or many stretches of DNA, even entire genomes and many genomes. The challenge has been that the instruments deliver--short reads—short readouts of sequence. What happens then is that scientists face the challenging computational task of stitching together short reads into contiguous sequence. But long-read sequencing is a way to address this challenge. 
The method of the year according to Nature Methods is: long read-sequencing. For a story I chatted with scientists at companies and in academia about long-read sequencing. This episode is with Dr. Jonas Korlach, chief scientific officer of Pacific Biosciences, which is one of the companies that offers instruments that can do long-read sequencing. 
(Art: J. Jackson. The following music was used for this media project:

Music:  Winnie the Moog, Funky Energetic Intro and Acid Trumpet by Kevin MacLeod Free download: https://filmmusic.io/song/3340-acid-trumpet License (CC BY 4.0): https://filmmusic.io/standard-license0 

Dr Uri Manor is a researcher at the Salk Institute who studies the dynamics of cells and Aly Putnam is a PhD student at University of Massachusetts in Amherst. They work in different fields and they are at different career stages. What they have in common is that they both have faced and continue to face adversity. They face an adversity of, the more invisible kind, because it's about their life in science as people with disabilities. They face adversity head on with strength, creativity and humor. 

(Art J. Jackson, Music: Funky energetic Intro by WinnieTheMoog. Another piece used in this media project: Paper Flakes by Rafael Krux. Free download: https://filmmusic.io/song/5695-paper-flakes License (CC BY 4.0): https://filmmusic.io/standard-license Artist website: https://www.orchestralis.net/)

Recently, we had the chance to get a sneak-peek of the meeting with the Society for Neuroscience's current leadership and to play a nerdy game with them. They are: Dr. Gina Turrigiano, Brandeis University researcher and current President of the Society for Neuroscience,  Dr. Robbie Greene of the University of Texas Southwestern Medical Center, current chair of SfN’s Public Education and Communication Committee and Dr. Damien Fair from the University of Minnesota, incoming chair of SfN’s Public Education and Communication Committee. If you want to register for the meeting, you can do so here: https://www.sfn.org/meetings/neuroscience-2022/registration .

And we played a nerdy game with them. It's 'we' because this podcast episode is co-hosted by Dr. Jean Zarate, senior editor at Nature Neuroscience, who is also a musician and an actor. This podcast series expands on the things I hear and read and offers conversations with people I meet in the course of my science journalism adventures.

(Art J. Jackson, Music: Funky energetic Intro by WinnieTheMoog. Another piece used in this media project: Legend of One by Kevin MacLeod: Free download: https://filmmusic.io/song/3973-legend-of-one License (CC BY 4.0): https://filmmusic.io/standard-license Artist website: https://incompetech.com)

This is a podcast series with some of the people I spoke with for a story about the creative grit scientists in The Global South apply in the fight against COVID-19. They collaborate, they network, they get creative to get what they need: supplies and strength for their research. In the haste to clinical trials for the COVID-19 vaccines some people were missed who need special attention. Thomas Egwang talks about why he and his colleagues submitted a letter to Nature Immunology about this and how research on this "quarter of humanity" continues.