Conversations with scientists

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.