Fernando De La Torre Blog 2

Summer Blog – Second Entry

I realized that I haven’t really talked about my summer research yet. In essence, the Monack Lab studies various angles of sepsis – a detrimental state of systemic inflammation due to overbearing bacterial infection in mammals. My mentor Sky Brubaker likes to look at a particular pathway that involves the protein ‘caspase-11’ – which complexes with other caspase-11 units inside the macrophage to form the ‘inflammasome’. The inflammasome is activated by intracellular Gram-negative bacteria (in the macrophage) or lipopolysaccharide (LPS). Once the complex is activated, it basically cleaves other downstream proteins (inside the macrophage) and terminates in a particular type of macrophagic cell death called ‘pyroptosis’. An extreme amount of pyroptosis throughout the body from a systemic infection causes sepsis, organ failure, and eventual death. In order to buy physicians time when treating patients with sepsis, my mentor wants to further understand the pathway and find its downstream targets, to potentially block pyroptosis with a therapeutic.

That being said, my project is based on two variants of caspase-11 that are found naturally in macrophages. We don’t know if these variants of caspase-11 also activate the inflammasome in the presence of LPS/Gram-negative bacteria. We set-out to make plasmid constructs containing these caspase-11 variants, and then insert them into a line of macrophages that don’t have a functional caspase-11 gene. I’ve hit a few set-backs over the last two weeks, so I’ll have to start my cell lines all over again. But once that’s complete, we can challenge the macrophages that have the caspase-11 variants with LPS and cholera toxin B (which simulates LPS entering the cytosol), and check for pyroptosis. Based on previous literature, our hypothesis is that the variants will not activate the inflammasome. This is a schematic that I made for a presentation I’m giving at the end of the summer:

I remember telling Dr. Long that I was going to take the time to learn Adobe Illustrator this summer, and so far, I have made excellent progress is making all my own figures and animations! It was a skill that I put-off way too long, and the entire MARC 2015-2016 cohort last year can attest to my struggle. My presentation skills are also improving, and I am looking forward to presenting my project in the fall to the new MARC 2016-2017 cohort!

Lastly, I have started exploring applications of linear algebra with a really cool graduate student that studies ‘anticipation’ in the brain when musicians play their instruments. He’s been opening up a new field for me in modeling and machine learning that can be applied to anything from genomics to big data. He has inspired me to continue learning how to code, on top of completing my statistics minor. This is the building where we hold our discussions on Friday nights; it used to be the Stanford University president’s residence before it became CCRMA – the Center for Computer Research in Music and Acoustics:

That’s all for now. As always, my regards go out to Dr. Long, Dr. Jones, Alfredo, Dr. Quinones, and Dr. Goins. Hope all is well in Los Angeles.

-Fernando