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Conversations with scientists
32 minutes | May 28, 2022
Creative grit: the Global South takes on COVID-19, Episode 2
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)
19 minutes | May 4, 2022
Ukraine and science, episode 2
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.
30 minutes | Apr 23, 2022
Ukraine and science, episode 1
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.
42 minutes | Apr 12, 2022
Creative grit: the Global South takes on COVID-19, Episode 1
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
62 minutes | Mar 25, 2022
The CRISPR Children, Episode 4
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.
53 minutes | Feb 3, 2022
Predicting protein structure, episode 4
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.
43 minutes | Feb 3, 2022
Predicting protein structure, episode 3
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.
36 minutes | Jan 11, 2022
Predicting protein structure, episode 2
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.
59 minutes | Jan 11, 2022
Predicting protein structure, episode 1
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
47 minutes | Jan 6, 2022
The CRISPR Children, Episode 3
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.
23 minutes | Dec 1, 2021
The CRISPR Children, Episode 2
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.
35 minutes | Nov 27, 2021
The CRISPR children, Episode 1
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.
20 minutes | Oct 30, 2021
Ask the crab
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.
41 minutes | Sep 24, 2021
Not lost in space Episode #2
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 accidentally sort of independent histories and building genetic tools. And then at the Allen, we sort of merged our forces, but both of us worked on building genetic tools. And then here we worked together on. Again, expanding and building new genetic tools, but for me, this is something that I've felt was always essential. You can define Cell types, you can define exactly where they are in the tissue, but you need to do something about them, right. To visualize them, but not only visualize them, you need to perturb them. And then you need to observe the effect that perturbation has on the organism. That's how you build causality. VivienAtlas-making and genetic tools in brain science are about analyzing cell types, knowing where they are in the brain, learning what the cells do, how they interact with other cells and how their activities lead to complex behavior such as memory. Part of this science undertaking is knowing which genes cells express where. Genes tune all sorts of things in the body and the brain, too. Genes might be turned off for a while, then be on and highly expressed. They might have low levels of expression or be silenced for some phases, expressions can shift. Knowing which genes are expressed where is at the core of spatial transcriptomics. Hongkui Zeng explains how spatial transcriptomics matters in brain development. [8:57] Hongkui ZengSo spatial transcriptomics is also critical for understanding development because during development, the number of cells, not only the number of cells is increasing. Right. And regions are growing, but also there are there is migration of cells, all kinds of cell types happening. And the and the cells migrating. They follow specific trajectories. Very often the cells migrate over their long distance from where they are born to their final location. So the state of the cells in development is often associated with the position of the cell during that path. There's a lot of migration happening. Think about your whole brain or your body comes from a single cell. And then there are always new cells are born and they are all organized in this beautiful structure. Cells are moving during development all the time. So you trace their past, then you understand, you know, that kind of relationship across time. VivienSpatial techniques can yield plenty of valuable information about the brain for Hongkui Zeng, it started nearly 20 years ago. Allen Brain Atlas And over time it’s become clear it’s hard to distinguish cell types. [10:28] Hongkui Zeng For me, it started with the Allen Brain Atlas on a Brain Atlas started in two thousand three. It's a in situ expression profiling of all the genes in the mouse genome, about 20-25,000 thousand genes in the mouse genome. It look at it, it looks at the anatomical spatial expression patterns one gene at a time. It’s a reference database th
31 minutes | Aug 8, 2021
Not lost in space Episode #1
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 they had this idea basically, I know, putting barcoded reverse transcription primers in an ordered fashion on a surface. And early on, they they brought in Fredrik as a master's student. At the time I was not involved. I was still writing my PhD thesis[00:08:11.110] - VivienAt the time. Fredrik Salmen was a master's student at KTH and Patrik Stahl was a Ph.D. student at KTH. He remained at KTH after his dissertation in 2010, then started on this project.[00:08:24.880] - Vivien During the gist of this project, Fredrik Salmen became a PhD student in Joakim Lundeberg lab at KTH and Patrik Stahl was a postdoc in Jonás Frisen's lab Karolinska Institute. This was a collaboration between University Labs[00:08:42.460] - Patrik StåhlScience for Life Laboratory, where we are sitting, that's a joint effort between the Royal Institute of Technology KTH and then Karolinska Institutet and Stockholm University, which means that we were all sitting together more or less. Jonas Frisen he had a separate lab also sort of up the hill, but quite close to where the rest of us were sitting.[00:09:10.420] - VivienThe approach the scientists developed involves working with fixed stained tissue and getting landmarks of gene expression.[00:09:19.120] - VivienThis is how it works. The tissue is imaged then treated so it becomes permeabilized. That process releases the mRNAs that move down and attach to an array that is below the tissue. This array holds barcodes. The mRNAs gets stuck in place. At the spots where they are fixed. The mRNAs are reversed transcribed, the tissue is dissolved and what you're left with is spatially barcoded, complementary DNA affixed to an array. Then you can use sequencing. When the complementary DNA is sequenced you get spatially resolved transcriptomics: the barcodes are identifiers for the mRNAs.[00:09:58.330] - Vivien So the platform tells you which genes are where because you have the original imaged tissue slide as a kind of reference. That's the Science paper. The team has set out with ambitious goals. They had wanted to capture them RNA from every cell in the tissue and they wanted a lot of other things. Here's Fredrik Salmen.[00:10:19.630] - Fredrik SalménWe really wanted to aim for single cell at the start. And this is I mean, now you can see this is not what we published in the end in 2016, we went for some kind of larger spots, around hundred micrometers. But early on, we really wanted to go down to that level and was very tricky because we didn't have the technology ourselves or the knowledge how to make them. So we had collaborations with companies and other gro
28 minutes | Jul 1, 2021
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.
33 minutes | Apr 28, 2021
Long-COVID Part 3: A chat with Terina Martinez
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.
37 minutes | Apr 28, 2021
Long-COVID Part 1: A chat with Nadia Rosenthal
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.
19 minutes | Apr 28, 2021
Long-COVID Part 2: A chat with Avi Nath
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.
27 minutes | Nov 13, 2020
A chat with with Na Ji
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.
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