Cogbites Interview Series: Nicolas Scrutton Alvarado

Welcome back to our cogbites interview series, where we interview cognitive scientists by asking them a few questions about their interests in science and what keeps them engaged both in and out of the lab.

As a reminder, you can learn a little about our own team of contributors by reading their bios (either on our author page or at the bottom of each post), but this is a chance to get to know some early-career scientists even better. Our last interview was with Alex Knopps, a second year Ph.D. student in Psychology and Discipline Based Education Research programs at North Dakota State University.

This week we interview Nicolas Scrutton Alvarado, a 4th year graduate student in the Department of Neurobiology at Northwestern University. Nicolas is pursuing his Ph.D. in molecular neurobiology with Dr. Yue Yang.

Nicolas studies the 3D organization of the genome, called chromatin architecture, in the context of cerebellar development. He is investigating how chromatin architecture changes over neural development, and how it in turn affects differentiation and maturation.

Nicolas Scrutton Alvarado

He recently wrote a blog post on cogbites about the role of our brain in our behavioral response to illness.

Here’s our interview with Nicolas:

Why did you decide to pursue cognitive science? 

I’ve always been fascinated in the intersection of environment and genetics. Exposure to neuroscience concepts during my undergraduate studies morphed that fascination to the impact of cognitive experience on molecular processes. I’m fascinated by the questions on how what we experience and feel have a tangible impact on our biology.

What are you currently working on?

I’m currently working on investigating the 3D movement of genes across brain development. The 3D localisation of genes in the cell nucleus, known as genomic architecture, has been shown to play a role in cell differentiation and gene transcription. I’m interested in how certain regions of the genome move across the development of cerebellar granule neurons, the most abundant cell type in the brain. This abundancy makes it a really attractive candidate for use in biochemical studies. Normally, isolating cells from the brain is difficult – the cell types can so diverse and rare, which makes identifying molecular information from them challenging. In the cerebellum, around 70% of the cells are granule neurons. That way, any experiment using the whole tissue is primarily gathering data from granule neurons. I’m interested in studying the changes in its genomic architecture because it’s a relatively new field, and we don’t know much about the mechanisms at play! The smaller scale structure of the genome, how different regions interact with one another to drive gene expression, are pretty well identified. By contrast, the mechanisms governing the movement of large sections of the genome, whole chunks of the chromosome, are unknown. That’s where my research sits.

We can study genome architecture through a couple of different ways. One way is using biochemical techniques called chromatin conformation captures, or 3C techs. You use a sort of glue to freeze cells in place, which means that bits of the genome that are close together in 3D are held there. The glue sticks those regions together, then you can cut the DNA into small bits and sequence them. Regions which are close together in 3D space will be sequenced together, which allows us to build maps of the 3D interactions in space. The 3C variant I use are called HiC maps (yes, named after the popular fruit juice).

The second way is a little more intuitive. It’s possible to tag regions of DNA with fluorescent markers, which means you can directly see their location inside cells (like below). From there, you can see how they move around each other, or how they interact with one another, and other things present in the nucleus. That’s the way I primarily study them.

An image of dissociated cerebellar granule neurons, stained with flourescent markers. The blue is Hoechst, a marker for general DNA. The red and green spots are different regions of the genome which I study.

What’s the most exciting concept in cognitive science?

I think the innovations in understanding the molecular mechanisms behind cognition and behavior are really exciting, and very important. It may hold the clues we need for the treatment of mental disorders, as well as a better understanding of how our brains work.

What sparked your interest in science communication (SciComm)?

I come from a family of journalists, so communication was always emphasized while growing up. I got a chance to explore science communication in my undergrad, where I wrote and edited for a student-run science magazine. From there, I’ve had a chance to develop my skills and attend to my interest in a number of ways, from writing to podcasting. I think science communication is an incredibly important aspect of science, and needs a greater emphasis in the scientific enterprise.

When I’m not working in the lab, I’m usually involved in some SciComm project! I’m a founder and writer for the mental health organization Mentally Minded, an editor for Northwestern’s Helix Magazine, the co-host of the science podcast In the Spotlight, and a contributing writer here at Cogbites!

Is there anything else you want us to know about you?

In my spare time, I like to cook new recipes, go rock climbing with friends, or read fiction (I do enough non-fiction in research papers). I’m particularly fond of baking breads – the recipe that sparked my love of cooking was attempting to make my own focaccia after a disappointing experience from one in a local supermarket in Scotland, where I lived at the time.