Conversations with scientists

This podcast was uploaded earlier this year but somehow it was deleted, sorry. So it's not quite a sneak-peek anymore...Whether or not you attended the  2024 annual meeting of the International Society for Stem Cell Research (ISSCR) or not, you might enjoy this conversation. It's with Dr. Amander Clark from the University of California at Los Angeles, she is also the current president of the ISSCR; Dr. Malin Parmar from Lund University and Dr. Agnete Kirkeby from the University of Copenhagen. They are program chairs of the ISSCR meeting. My co-host is manuscript editor Dr. Stylios Lefkoupolos from Nature Cell Biology.

The annual meeting of the American Society of Human Genetics (ASHG) is about to start. Here's a sneak-peek of the meeting with Dr. Bruce Gelb who is the current president of ASHG, he is also a researcher at the Icahn School of Medicine in New York City. My co-host --Dr. Mike Fletcher senior editor at Nature Genetics-- and I, asked Bruce Gelb about the meeting but also about some trends such as genetics and inclusion, biobanks, sequencing of the genomes of newborns, exposomics and more. 

Hear about some of the presentations at the upcoming 2024 annual meeting of the Society for Neuroscience. This sneak-peek that also is ab out some of the latest trends in neuroscience is with Yale University researcher Dr. Marina Picciotto, who is also the president of the Society for Neuroscience and Dr Damien Fair from the University of Minnesota. He is the chair of the Public Education and Communication committee of the Society for Neuroscience. 

Stem cells are intriguing cells with a lot of flexibility in their biographies. And these cells are the focus of the annual meeting of the International Society for Stem Cell Research, ISSCR. It's happening soon: in July. Here is a sneak-peek of the meeting with the ISSCR leadership: Dr. Amander Clark from the University of California at Los Angeles, she is the current president of the ISSCR. Dr Malin Parmar from Lund University and Dr Agnete Kirkeby from the University of Copenhagen. They are program chairs of the ISSCR meeting. Co: host: Dr. Stelios Lefkoupolos from Nature Cell Biology (Art: J. Jackson, Music: Episode 6 by Walz; Sound effects: Laidback Lunch, both licensed from artlist.io..)

This podcast is with Dr Sethuraman Panchanathan who directs the US National Science Foundation. He talks about his nickname, about AI and data science, about training AI models, about transparency, about the language of collaboration, competitiveness, about talent. He says: "I think what we need as a nation is not only to unleash every ounce of talent in our country, the domestic talent, at full force and full scale. And we should welcome and aggregate and retain every ounce of global talent at full force and full scale."  (Art: J. Jackson, Music: Golden Era by Steven Bedall and licensed from artist.io.)

Can you be a scientist and parent? Of course. But it's not always easy. Dr. Ying Diao is at the University of Illinois Urbana Champaign is in the chemical and biomolecular engineering department. She has a stack of awards, a lab and two children. She talks about her research, for instance a project focused on wearable electronics for plants, that tracks their growth and well-being. The idea came to her during her pregnancy. She talks about deciding to have children and the reactions of those around her. And she describes which conferences have lactation rooms and which do not. (Art: J. Jackson, Music: Bubbles by XiMo, licensed from artlist.io)

This episode is about dirt or, phrased more scientifically, soil. It's about soil health, soil biodiversity and ecology. It's a conversation with Dr. Ciska Veen, soil and ecosystems researcher at the Netherlands Institute of Ecology and Dr. Wim van der Putten, who heads terrestrial ecology at the Netherlands Institute of Ecology. (Art: J. Jackson; Music: Jungle Jam by Evert Z, licensed from Artlist.io.)

Jean King, who is the dean of arts and sciences at WPI-Worcester Polytechnic Institute in Worcester, Massachusetts, talks about what Nobel Laureate Katalin Karikó means to her and about persistence and success in science. (Art: J. Jackson; Music: Towers by sero, licensed from artlist.io)

What good does it do to start a big research project? How do you get it to soar? Dr. Anna Barker has some answers about that from the past, the present and the future. She is chief strategy officer at the Ellison Institute, a think tank and research institute. Before that, she was the principal deputy director of the US National Cancer Institute and deputy director for strategic scientific initiatives there. One of her projects is The Cancer Genome Atlas, co-directed with Dr. Francis Collins. This episode will be about cancer. Cancer is upsetting, of course, but this episode might feel empowering. The podcast is also about academia, physics, information theory, big data, history and science policy. (Art: J. Jackson. Music: Michael Drake - Solstice licensed from artlist.io) 

The Society for Neuroscience annual meeting, a big conference in neuroscience, is about to start. This year, it's in Washington. And here is a sneak peek of the meeting for you. Along with editors at Springer Nature, I got the chance to ask a bit about the meeting before it starts shortly. It was a mash up of a press conference of sorts and a wider discussion with colleagues from Scientific American and from Nature Neuroscience. In this podcast episode, you will hear questions from them and from me and responses by Dr. Oswald Steward, the president of the Society for Neuroscience (SFN) and Dr. Damien Fair who is the chair of the SfN Public Education and Communication committee. (Art J. Jackson) (Music: Billiard Balls by Raw, licensed from artlist.io)

Science and academia need diversity. Easier said than done because, for example, many students face housing insecurity, which keeps them from a focus on their studies. But that's something students are trying to change. I spoke with current and former students at UC Santa Cruz about this. In this episode you will hear from Abbi Cundall, Natalie Clifford, Emerald Waters, Zennon Ulyate-Crow and Nicolas Robles. (Art: J. Jackson, Music: Nonsense by Raw licensed from artist.io)

Labs and a lab's team members often speak many languages. Science is international. But in a lab environment languages can set people apart. I wrote a story about lab languages for Nature Methods here: https://rdcu.be/doPnv There's a blog post here: https://cellmolbiocommunity.springernature.com/posts/podcast-lab-languages . And here is more from that story. It's a conversation with Dr. Denis Wirtz, a cancer researcher at Johns Hopkins University and Johns Hopkins School of Medicine and vice-provost for research at Hopkins. (Music: Better by Dizzy, Art J. Jackson)

Dr. Liz Bradley, who is on the computer science faculty at the University of Colorado Boulder, is an athlete-scientist. She is a mathematician and a former Olympic rower. In this podcast you will hear about her, about sweeping and sculling, about rugby, why it's good to have a notebook, about data analysis and some pitfalls that can happen in data analysis when you use software analysis but don't know exactly what the tools do and about the importance of whitespace. (Art: J. Jackson, Music Freerolling by T. Bless and the Professionals licensed from Artlist.io)

Science and the arts have much to say to one another. This episode is a conversation between scientists and artists, between scientists who foster the arts through fellowships and residencies and artists active in science and people who live in both worlds: science and the arts. All this makes for interesting and sometimes challenging groups of identities. With: London-based artist Charlotte Jarvis, Designer, now medical student Mika Futz, Jean Mary Zarate, editor with Nature Neuroscience, musician and actor, Catherine Musselman and John Rinn, genetics researchers at University of Colorado, proteomics researcher Albert Heck. (Art: J. Jackson, Music: David Gives, Views from Palermo licensed from artlist.io) 

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. 

A conversation with sailor-scientist Romain Troublé Tara Ocean Foundation. He is executive director of the foundation devoted to the ocean and ocean research. And there's a connection to the French fashion house agnès b. You have perhaps heard of the gut microbiome, the many microbes in our gut that play a large role in maintaining our health. The ocean microbiome plays a similar role in our planetary health. A massive research effort is underway to better understand the roles the ocean's microbiome plays. 

Models are important tools: they resemble, they mimic, they imitate something to a greater or lesser extent. How similar models are to the 'real thing' is usually a challenging  issue. And it's a big issue with stem-cell derived models of the human embryo.These embryo models, models of the embryo's 8-cell stage, of the blastocyst or of the gastrula are emerging and they are ones that labs can use to characterize the molecular and physiologic events that take place during early embryogenesis. My story in Nature Methods about some of these embryo models is here. For this story, I spoke with Christine Mummery, a researcher in the anatomy and embryology department at Leiden University Medical Center. In this podcast, she talks about models of the blastocyst and the gastrula, about the updated International Society for Stem Cell Research (ISSCR) guidelines, and shares some thoughts about about what is involved when assessing a model. "If I'm claiming this is a liver cell, what does it have to show? And this is a tricky, tricky thing," says Christine Mummery. 

I asked Dr. Leo Poon, who co-directs the Hong Kong University Pasteur Research Pole, if he has a fleet of private jets. He does not. But he wishes he did. He and his team have helped colleagues all over the world on COVID-19. He and his team developed a diagnostic assay quite soon after the genome sequence of SARS-CoV-2, the virus that causes COVID-19 became known. His is the lab that detected and identified  SARS, the outbreak in 2003. And many other viruses. Like most science journalists, I report on COVID-19 and I had been wondering about researchers in the Global South and their COVID-19 related research. Here is the story I did for Nature Methods https://www.nature.com/articles/s41592-022-01439-w. For that story, I spoke with Leo Poon about his work during the height of COVID-19 and now and his outlook for the future. This podcast is more from that conversation. (Art: J. Jackson)

How is the Russian invasion of Ukraine affecting scientists? Here is another episode on this with a conversation with Dr. Svitlana Dekina, a researcher at the A.V. Bogatsky Physico-Chemical Institute of the National Academy of Sciences of Ukraine in Odessa, Ukraine. She has recently left Ukraine and is now at the European Molecular Biology Laboratory in Heidelberg, Germany. She is in Germany with her children; her husband is still in Ukraine. It's not easy to talk about staying and leaving but I am grateful Dr. Dekina took a moment to chat. And her colleague Dr. Theodore Alexandrov, an EMBL researcher did some translating--thank you! The passages in Ukrainian/Russian are also in the podcast. But Dr. Dekina speaks English just fine.  

The Russian invasion of Ukraine is affecting scientists in many different ways. Here is a conversation with Dmytro Gospodaryov, a researcher in the department of biochemistry and biotechnology at  Vasyl Stefanyk Precarpathian National University in Ivano-Frankivsk, West Ukraine. I spoke to him shortly after the Russian invasion in Ukraine began. And it feels like that was so very long ago. He is ok and safe and still in Ukraine with his family. 

Virologist Dr Marycelin Baba from the University of Maiduguri in northeastern Nigeria is passionate about her work on viruses, She runs a World Health Organization (WHO)-accredited and WHO-sponsored lab where the team has worked, for example, on polio. When COVID-19 emerged, she and her team were prepared and she was called upon to help build capacity in Nigeria to address COVID-19. When the government asked her to certify a lab not up to biosafety levels, she said no. "Even if I was to be killed, I don't mind," she says. This is episode 1 of a series of podcasts about the grit and determination scientists in the Global South are putting to work against COVID-19. It's not, in my view, a downer of a story. It goes along with a feature I did for Nature Methods called 'Lessons from the Global South's fight against COVID-19.' That story is here: https://www.nature.com/articles/s41592-022-01439-w

Around three years ago, three children were born with genomes edited before their birth. They are supposedly doing ok, sources tell me. But it's hard to know for sure. Germline-genome editing is not permissible in most countries, but it might one day be performed to avoid heritable diseases that are incurable. But the technology needs to be much more precise than it is now. In this episode, I speak with Dr. Alison van Eenennaam of the University of California, David about her work in cattle and we also talk about germline-gene editing in people. She talks about Cosmo, the first bull with a gene added to his genome. And she talks about her thoughts on applying germline gene-editing in people and about the offering, by some companies, promising parents-to-be 'designer babies.'Note: Some cautions for you. If you don't like meat, you might not like this podcast. Although you might want to hear about projects related to livestock health and breeding in the tropics or about reviving and restoring endangered species. You might not like this podcast if you do not want to hear about animal experiments. Although we do also know that many things intended for use in people are tested in animals first. And that is indeed fraught. Even if you have aversions of this kind, I would like to invite you to tune in to hear more about Alison van Eenennaam's work. 

This episode is about AlphaFold and the impact it is having on junior scientists. I spoke with a group of them from different labs at the Max Planck Institute of Biochemistry. I spoke with Dr Isabell Bludau, a postdoctoral fellow and computational biologist in the lab of Dr Matthias Mann, Dr. Bastian Bräuning, a postdoctoral fellow and project group leader in the Department of Brenda Schulman and Juan Restropo a PhD student in the lab of Dr Jürgen Cox. 

Biology and AI for predicting protein structure. This is a chat with conversation with some members of the Rost lab  at the Technical University of Munich. Dr. Maria Littmann, postdoctoral fellow, and PhD students Konstantin Weissennow and Michael Heinzinger and Dr Burkhard Rost, principal investigator.  We talked about AlphaFold, a computational approach from DeepMind Technologies that has changed the way and the speed at which proteins can be predicted. 

Protein structure prediction is the Nature Methods Method of the Year for 2021.  Here is my feature on that. https://www.nature.com/articles/s41592-021-01359-1    For the story, I chatted with Helen Berman, co-founder of the Protein Data Bank (PDB), which is home to experimentally determined structural data for over 180,000 proteins. What's next for the PDB. And of course this relates to the past. She's a bit secretive about the future, but discloses some of the plans currently underway. She is co-architect of the PDB's next chapter. 

Proteins are twirly, curly, dynamic structures. Crucial for life, complicated to study. Predicting protein structure has been tough but it's now easier as AlphaFold enters the scene. That doesn't mean that AlphaFold has solved all challenges, of course. AlphaFold was developed by DeepMind Technologies, a company that was bought by Google in 2014. Lots of protein puzzles remain. Dr. Janet Thornton from the European Bioinformatics Institute and Dr David Jones of University College London talk about what AlphaFold can do and what it cannot yet do. They look forward, backward and all around on this subject. He says, laughing, he has "extreme cautious optimism" about the prospects of this field. You can also find my feature story about protein structure prediction, which is the Nature Methods method of the year for 2021, here: https://www.nature.com/articles/s41592-021-01359-1 

To go along with my investigative story The CRISPR Children in Nature Biotechnology, I am producing a rolling series of podcasts. This episode is a chat with Dr. Eben Kirksey, an anthropologist at Deakin University, which has campuses in and near Melbourne, Australia. He has written a book called The Mutant Project, Inside the Global Race to Genetically Modify Humans.  It's dedicated to Lulu and Nana, two of the three children who are known to have had their genomes edited before their birth. Their birth in 2018 caused a global uproar. there is also a third child, whom I call Amy, who also has a gene-edited genome. Dr. Kirksey talks about the lab that brought them about and offers some background about the social, political, cultural aspects that made the experiments possible. 

The CRISPR Children is a podcast series about the children whose genomes were edited before their birth in 2018. The podcasts accompany a story I did about these children in Nature Biotechnology by the same name. You can find the story here: https://rdcu.be/cB7Nx  The children were born somewhere in China. They came about due to experiments performed in the lab of He Jiankui at Southern University of Science and Technology in Shenzhen. These were unethical experiments. How are the children? And how could you assess their health and possible future risks? And why are they genetically mosaic? There is a lot of secrecy and rumor about these children. One has to maintain their privacy and dignity. They are celebrities and victims. They and their parents might be helped if the biomedical community tried to understand more about the experiments. But that is far from straightforward. Especially because many scientists declined to talk about them. But a number of them kindly did speak with me and I am grateful for that. Here is some of what I heard.       

The CRISPR Children is a series of podcasts about the children whose genomes were edited before their birth in 2018. The podcasts accompany a story I did about these children in Nature Biotechnology by the same name. You can find the story here: https://rdcu.be/cB7Nx  The children were born somewhere in China and the result of experiments performed in the lab of He Jiankui at Southern University of Science and Technology in Shenzhen. These were unethical experiments. But how are the children? And how could you assess their health and possible future risks? There is a lot of secrecy and rumor about these children. One has to maintain their privacy and dignity, of course. But they are also victims. They and their parents might be helped if the biomedical community tried to understand more about the experiments. But that is far from straightforward. Especially because many scientists declined to talk about them. But a number of them kindly did speak with me and I am grateful for that. Here is some of what I heard.  This episode is with Dr Kiran Musunuru of the University of Pennsylvania, a physician-scientist who works in genetics and gene-editing. He has also co-founded a company called Verve Therapeutics. He has written a book about the children called: The CRISPR generation The Story of the World's First Gene-Edited Babies.

Neuroscientists use models of the brain to study the brain. One of those model types: organoids. One way to get a conversation with a neuroscientist started badly is to ask them about the 'mini-brains' in the dish on their lab bench. It's not that the blob in the dish doesn't somehow look like a piece of living tissue that could be a piece of brain. Or that this blob isn't relevant to studying the brain. It is. Organoids are grown from stem cells that were coaxed to become neurons. They differentiate and grow into a three dimensional object. And these objects are becoming more complex and more dynamic in labs around the world. Dr. Eve Marder from Brandeis University talks about what organoids can tell researchers about the brain and what they might be less suited for. And why they are biological theory. 

This podcast is with Dr. Hongkui Zeng who directs the Allen Institute for Brain Science and Dr. Bolisjka Tasic who directs Molecular Genetics at the Allen Institute for Brain Science. It's about how spatially resolved transcriptomics, a Nature Methods Method of the Year, can help to understand the brain. I did a story about it here: https://www.nature.com/articles/s41592-020-01033-y . This is a podcast series that shares more of what I found out in my reporting. The piece is about smoothies, fruit salads, fruit tarts, genomics and a big puzzle called: the brain. Transcript of podcast Note: These podcasts are produced to be heard. If you can, please tune in. Transcripts are generated using speech recognition software and there's a human editor. But a transcript may contain errors. Please check the corresponding audio before quoting.Not lost in space Episode 2 Hi and welcome to Conversations with scientists, I'm Vivien Marx. This podcast is about space--space in biology, actually. Talking about the role of space and spatial analysis in biology is a chat about food. About smoothies, fruit salads and fruit tarts. Here's Dr. Hongkui Zeng and Dr. Bosiljka Tasic from the Allen Institute for Brain Science. [0:30] Bosiljka Tasic Fruit salad and smoothie. Fruit tart is spatial transcriptomics.Smoothie is Bulk RNA-seq. Ok passé Hongkui ZengForget it.  Bosiljka Tasic You have fruit salad, you have dissociated cells you are profiling, you have lost the context, you have a context in the piece of tissue you have dissected. Then there is the fruit tart. You know exactly where each piece of fruit.  Relationship to the other VivienOk so spatial analysis in genomics is understanding a fruit tart. Knowing which genes are expressed where and what the relationship is of the genes to one another. The two scientists will talk more about this shortly. There's Dr. Bosiljka Tasic, she directs Molecular Genetics and her research is for example on cell types in the mouse brain. And Dr. Hongkui Zeng who is director of the Allen Institute for Brain Science. Before they explain more about this science, here they both are, kindly teaching me how to pronounce their names. As ever I will try to do this right. And likely fail.  [1:37] Bosiljka Tasic and Hongkui ZengI'm Bosiljka Tasic. Bosiljka Tasic. OK, got it   Hongkui Zeng. You don't pronounce the G at all, just, well, Zen, yeah, Zen G Zen. Yeah, yeah. It's very, very almost not there.   How would you how would you pronounce that if you emphasize the G . ZengG. So I think g you hear much more but it's not the correct way. I mean I've given you my Americanized way of saying my name. I see. Well I'm going to, I'm going to do it wrong anyway. But but at least for me, don't  worry. VivienNext, before we get back to their thoughts and research, just a bit about this podcast series.  In my reporting I speak with scientists around the world and this podcast is a way to share more of what I find out.  This podcast takes you into the science and it's about the people doing the science. You can find some of my work for example in Nature journals that are part of the Nature Portfolio.  That's where you find studies by working scientists and those are about the latest aspects of their research. And a number of these journals offer science journalism. These are pieces by science journalists like me.  This podcast episode about space in biology harkens back to interviews I did  months ago. Back then I asked scientists about their work and their thoughts about spatially resolved transcriptomics, which is a Nature Methods method of the year. In my slow pokey DIY podcast production this is episode 2 in a series about this field of study.  Spatially resolved transcriptomics helps with studying the brain, which is the giant puzzle that Hongkui Zeng and Bosiljka Tasic work on. Among their daily puzzles is: How many different cell types are there in the brains of mammals such as mice, primates or humans? There are lots of them.   And scientists want to be more precise than just saying there are lots of cells, of course. They want to know which ones there are and where they are. In the brain, another puzzle is where are cell types when. Cells are born and then often move to other areas of the brain where they will tend to all sorts of tasks. It takes a number of techniques to address these questions, including spatial techniques.  The US National Institutes of Health—NIH--has many research projects, one of them is the Brain Initiative, NIH's Brain Research through Advancing Innovative Neurotechnologies Initiative.  Part of that is the NIH Brain Initiative Cell Census Network (BICCN). One big BICCN project is to build a high quality atlas of cell types in the entire mouse brain.  Many labs are working together to produce human, mouse and non-human primate brain atlases, these are intended as references for labs around the world. The scientists use imaging, electrophysiology and molecular genetic analyses including analysis of gene expression, which is transcriptomics.  BICCN phase 1 is underway and phase 2 is getting underway. The project has started with the mouse brain and is moving toward an atlas of the non-human primate brain and the human brain.  One big challenge in this venture is distinguishing cell types. Cells may look very different but they might also look quite similar to one another. Here is Hongkui Zeng talking about BICCN [5:20] Hongkui ZengWe are currently in phase one, BICCN phase one, building this brain-wide cell type reference atlas. We are doing quite well and we expect to complete phase 1 in the next two years. And then phase 2 is starting, BICCN, phase 2 what you heard at SfN. There are several major themes for phase 2 that were announced by NIH. The three major themes are building cell-type targeting tools, moving into the study of primate brains including human brain, cataloging cell types in the human brain and then finally studying the connections, the connectomics of the human brain. Bosiljka is very active in one of those initiatives, which is building in one of cell type targeting tools  Bosiljka Tasic You want to define a cell type first, but then you want to be able to access it for experimental examination perturbation. You want to form causality connections between a cell type and, let's say a specific behavior. So in order to do that, you need to build usually a genetic tool that is based on genes that are expressed in the cell type or maybe regulatory elements, enhancers that are active in that cell type. You can you can create a transgenic mouse or a viral tool that will then deliver a particular transgene, a particular perturbing or labeling gene to that cell, and then you can visualize the cell, monitor it, maybe monitor its activity or perturb it and ask for  Phenotypes effects at the level of that cell, at the level of the circuit, at the level of the whole organism. And both Hongkui and I, we are we have a just...

This podcast is about two scientists, Dr. Patrik Ståhl and Dr. Fredrik Salmén, who are joint first authors of a paper that kickstarted a field. It's about finding work they did with colleagues to enable finding out where in tissue gene expressions is happening. It's called spatially resolved transcriptomics. It is a Nature Methods Method of the Year and I did a story about it here: https://www.nature.com/articles/s41592-020-01033-y . This is a podcast series that shares more of what I found out in my reporting. The piece is about patience, stamina, friendship, surfing the Baltic Sea, genomics and imaging. [00:00:05.560] - Vivien MarxHi and welcome to Conversations with Scientists, I'm Vivien Marx. This podcast is with and about two scientists and about space space in biology. Actually, you'll meet Patrik Ståhl. He's on the faculty of KTH Royal Institute of Technology in Stockholm, Sweden, and Fredrik Salmén, who is currently a postdoctoral fellow at Hubrecht Institute in the Netherlands. They will talk about a field.[00:00:33.280] - Patrik StåhlThe whole field. It's really it's it's an awesome field.[00:00:36.940] - Vivien That's Patrik Ståhl. Their work led to a major publication in the journal Science, and they are both joint first authors of this paper,[00:00:47.710] - Patrik StåhlWe share the honor[00:00:47.710] - Fredrik Salménand the pain.[00:00:47.710] - Vivien The honor and the pain. That's research for you. Just briefly, before we get to that about this podcast series, in my reporting, I speak with scientists around the world, and this podcast is a way to share more of what I find out. This podcast takes you into the science, and it's about the people doing the science. You can find some of my work, for example, in Nature journals that are part of the nature portfolio. That's where you find studies by working scientists.[00:01:19.960] - Vivien And those are about the latest aspect of their research in a number of these journals offer science journalism. These are pieces by science journalists like me. This podcast episode is one of several I'm producing about space in biology. Months ago, I interviewed researchers who work on Spatially resolved transcriptomics for a story and in my slowpokey DIY podcast production. This is part one in a series about this field of study. So Patrik Stahl and Fredrik Salmen here they are introducing themselves to help me learn how to pronounce their names.[00:02:02.890] - Patrik Ståhl Fredrik you go first.[00:02:03.560] - Fredrik SalménFredrik Salmén. [00:02:12.290] - Vivien All right. I have to practice. OK, so in[00:02:16.750] - Patrik StåhlEnglish it's Patrick. It's Patrik Stahl.[00:02:21.650] - Vivien Patrick Sahl?  So no t, Stahl[00:02:29.210] all right, you have to brace yourselves.[00:02:33.980] - Patrik StåhlStahl means steel in English,[00:02:36.393] - Patrik StåhlPatrik Ståhl[00:02:36.780] - Vivien Wow I apologize . Despite their lessons, I am doing the Swedish pronunciation of their names badly. I hope they and Sweden will forgive me. So I interviewed these two Swedish scientists together and when we started to chat, I noticed a poster on the wall behind Fredrik Salmen. It showed a surfer riding a big wave. So I asked about that.[00:03:03.530] - Patrik StåhlFredrik actually quite advanced surfer, like wave surfer  at the time when we started this project.[00:03:14.540] - Fredrik SalménYah, it's true. Oh, it's actually me.  It's a little bit self-centered, I guess, to have their own picture on the wall. But it's fun, though. It's[00:03:27.620] - Vivien where was this taken?[00:03:30.290] - Fredrik SalménThis is actually Sweden. So it's the Baltic Sea.[00:03:35.900] - VivienThe Baltic Sea is cold. You need to wear a special suit if you want to surf there.[00:03:41.240] - Fredrik SalménYeah. It's like a frog suit with hood and gloves and boots.[00:03:45.920] - VivienSo do you still do this or.[00:03:48.320] - Fredrik SalménYeah, I still do. I'm a little bit, I would say much less nowadays and I'm also a little bit heavier these days, so not as agile anymore. But still when I get the opportunity I try to surf, it's nice. [00:04:06.020] - Vivien The two researchers worked together along with many others, but their connection was quite intense and you will hear more about that in this podcast.[00:04:13.260] - VivienIt was work that took around six years and led to a publication in the journal Science. And that publication kick-started a field. And there was a company spin out to the field of study is called spatially resolved transcriptomics, and it was crowned a Nature Methods method of the year. In this area of spatially resolved transcriptomics, scientists want to know where something takes place. It's part of understanding larger issues, such as why does the head grow where it does?[00:04:44.750] - Vivien Why does a part of the brain develop where it does? Why does a tumor grow where it does? It's genes that tune such events, genes are turned on or off, they are expressed at high levels or low levels or silenced, their expression can shift. With gene expression, it's like tissues are playing a kind of music, just one you need to find ways to hear. Patrik Stahl and Fredrik Salmen and their colleagues found one way to do just that.[00:05:15.370] - Vivien The work took place in Sweden. It involved surfing the cold waves of the Baltic, as you just heard. It's about friendship. It's about patience, about science, careers. If you're interested in any of that, as well as biology, genomics and imaging, please stick around. So this work in particular took six years and Fredrik Salmen and Patrik Stahl worked intensely together. They are the first authors of this paper in Science published in 2016, and it led to a company called Spatial Transcriptomics.[00:05:45.790] - Vivien What these scientists and their colleagues developed was a way to see where, for example, in a tissue genes are expressed. It's not the first way to do this, but it was a way to analyze a lot of mRNAs, a lot of gene transcripts at the same time. To understand why this matters, we can step back for a moment and consider a practical example that they told me about. A pathologist gets a tissue sample. It might be from a person who was just on the operating table.[00:06:13.300] - VivienThe tissue is prepared with chemical stains and then studied. The pathologist interprets what is going on in this tissue. Sometimes pathologists look at many tissue slides from many patients and want to compare them. In other cases, it is information that has to travel quickly to determine how a patient might need to be treated. Or the analysis is for a basic research lab that is studying a particular disease or development. As Patrik Stahl explains, scientists can look at a tissue slide and use stains and dyes to see what is happening there.[00:06:46.630] - VivienWell, sort of. This immunohistochemistry doesn't always answer all the questions of pathologist or other scientists might have[00:06:55.990] - Patrik StåhlSo I think this was like late 2009 and it was Jonas Frisen, who is a who is, s stem cell professor working at Karolinska Institute who is subjected to this kind of immunohistorchemistry a lot during his daily work. And I think that he was the one who first grew tired of a lack of spatial information that they could get out of a stain. And so late 2009, he contacted  Joakim Lundeberg and they together in early 2010, initiated this project , trying and then...

Marine echinoderms speak to developmental biologist Dr. Paola Oliveri at University College London for many reasons. Their evolution of a novel body plan is one of them. In a conversation she talks about teaching evolution, her training, her students and her love of science. 

COVID-19 has been bad. Many, likely millions of people, who have survived their COVID-battle, face a difficult array of symptoms. Breathing problems, joint pain, heart palpitations, brain fog are a few of them. This is part 3 of a three-part podcast series on long-COVID. This episode is a conversation with Dr. Terina Martinez, a field application scientist at Taconic Biosciences, which develops and sells mouse models. She talks about the challenges and possibilities of modeling long-COVID. There is also an article in Nature Methods to go along with this podcast series. 

COVID-19 has been bad. Many, likely millions of people, who have survived their COVID-battle, face a difficult array of symptoms. Breathing problems, joint pain, heart palpitations, brain fog are a few of them. This is part 1 of a three-part podcast series on long-COVID. You can also find my piece in Nature Methods on long-COVID here. Dr. Nadia Rosenthal, who directs science at the Jackson Laboratory, and her team are working on ways to model this diversity of symptoms, which can help figure out what is amiss in long-COVID and indicate how one might treat it. 

Around the world, COVID-19 has been awful. Many, likely millions of people, who have survived their COVID-battle, face a difficult array of symptoms. Breathing problems, joint pain, heart palpitations, brain fog are a few of them. This is part 2 of a three-part podcast series on long-COVID. This episode focuses on brain fog, one of the difficult symptoms of long-COVID. It's a conversation with neuroimmunologist Dr. Avi Nath, who is intramural clinical director of the National Institute for Neurological Disorders and Stroke (NINDS) at the US National Institutes of Health (NIH). There is a story in Nature Methods to go along with this podcast about long-COVID.

She's driven by curiosity. Na Ji is a physicist and neuroscientist at University of California, Berkeley. She develops ways to study the brain and she reads voraciously. She seeks to capture the signals that neurons pass to another with imaging and in multiple brain regions. She also teaches a class for people interested in physics. She calls it 'Physics for Modern Citizens. 

This episode of Conversations with ..Scientists--Bye-Bye Bunny-- is about research into diseases such as COVID-19 and neurological diseases, too. It's about the antibodies in our bodies. And it's about research antibodies. And it explores the possibility of perhaps generating and producing research antibodies without the use of animals.  It includes Dr. Alison Gray from Afability and the University of Nottingham, Dr. Katie Crosby from Cell Signaling Technology, Dr. Alejandra Solache from Abcam, Dr. Carl Ascoli from Rockland Immunochemicals, Dr Andrew Bradbury from Specifica, Dr. Achim Knappik from Bio-Rad, Dr Aled Edwards from the University of Toronto, Dr. Fridtjof Lund-Johansen from Oslo University Hospital, and Dr. Peter McPherson from McGill University. 

Pipelines are basically a series of steps. Algorithms are linked to one another, the output of one algorithm is the input to another. Pipelines can be simple and pretty complex. And maintenance of pipelines also ranges from simple to complex. They can run like a dream, they can get stuck, they can break. To talk about trends in this area, I sat down, virtually that is, with two scientists at DNAnexus: John Ellithorpe who is DNAnexus executive vice president and chief product officer and George Asimenos chief technology officer at DNAnexus. 

Part I of the annual meeting of the American Association for Cancer Research—it was all virtual—had 61,000 attendees. Part II is about to start. Here's a sneak peek about the meeting, its hundreds of talks and thousands of posters. Virtual conferences mean less of a carbon footprint, maybe a broader reach and a chance for attendees who cannot typically travel to AACR to attend virtually.  Commenting on AACR II and about virtual conferences more generally: Dr. Elaine Mardis: the current president of the American Association for Cancer Research. She is co-Executive Director of the Institute for Genomic Medicine at Nationwide Children's Hospital and the Nationwide Foundation Endowed Chair in Genomic Medicine. And Dr. Antoni Ribas, the incoming AACR president. He is at the University of California Los Angeles. He directs the Tumor Immunology Program at the Jonsson Comprehensive Cancer Center and is director of the Parker Institute for Cancer Immunotherapy Center at UCLA. 

Part I of the annual meeting of the American Association for Cancer Research was all virtual. There were 61,000 attendees, including some job-hunters. I wonder how this year's conference that is about to get underway will affect job-hunting.  This episode is with scientists talking about their hopes and allergic points as they job-hunt. It's based on conversations with job-hunters last year and this year. The guests on this episode are: Dr. Antonio Ward of the University of South Alabama, Melat Gebru from Penn State University, Paul Tran from Augusta University and Dr. Sadr-ul Shaheed from the University of Bradford. 

Today's episode is with and about Hui Yang. Dr. Yang is a researcher at the Institute of Neuroscience at Shanghai Institutes for Biological Sciences, which is part of the Chinese Academy of Sciences.  He has developed new base-editor variants. Base-editing is a kind of gene-editing. Overall the result led to base-editors with fewer off-targets, high on-target efficiency and a narrowed editing window, fewer indels and  fewer off-targets, he says. Yang sees a lot of promise for these base editors for both DNA and RNA base editing. Yang is a die-hard Manchester United. Among other aspects, he talks about how he organizes his lab for open communication. He is modeling the the culture of the Jaenisch lab at The Whitehead Institute. That's where Yang was a postdoctoral fellow. 

Proteins in a cell don't tend to practice social distancing. They have many associates but capturing all of the associates in one experiment is difficult. Dr. Carol Robinson and her team developed a way to be able to dissociate such complexes in a mass spectrometer and look at them in one experiment. It's a new kind of mass spectrometer and one she and her team co-developed with Thermo Fisher Scientific. Robinson is the first female professor of the University of Oxford, previously the first female professor of the University of Cambridge and she was appointed Dame Commander of the Order of the British Empire. This is a story about her by Vivien Marx.