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 Zeng

Forget 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

Vivien

Ok 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 Zeng

I'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.

Vivien

Next, 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...