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.
Feb 03, 2022•53 min•Ep. 21
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.
Feb 03, 2022•43 min•Ep. 20
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-a...
Jan 11, 2022•36 min•Ep. 19
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 abou...
Jan 11, 2022•59 min•Ep. 18
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. Th...
Jan 06, 2022•47 min•Ep. 17
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 h...
Dec 01, 2021•23 min•Ep. 16
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...
Nov 27, 2021•35 min•Ep. 15
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 differen...
Oct 30, 2021•20 min•Ep. 14
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, fru...
Sep 24, 2021•41 min•Ep. 13
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 ...
Aug 08, 2021•31 min•Ep. 12
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.
Jul 01, 2021•28 min•Ep. 11
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...
Apr 28, 2021•33 min•Ep. 10
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 ou...
Apr 28, 2021•37 min•Ep. 8
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 Neuro...
Apr 28, 2021•19 min•Ep. 9
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.
Nov 13, 2020•27 min•Ep. 7
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, D...
Aug 06, 2020•57 min•Ep. 6
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 A...
Jun 27, 2020•28 min•Ep. 5
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 ...
Jun 22, 2020•9 min•Ep. 4
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 G...
Jun 22, 2020•14 min•Ep. 3
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 fo...
Jun 07, 2020•10 min•Ep. 2
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 fem...
May 03, 2020•11 min•Ep. 1
