Blog Archives


Watching the Mice DANNCE

Over the past few years, the lab has been working on developing an imaging box, which takes multi-angle videos of mice in a box, observing their locomotion and other behavior. It provides a way for us to more accurately quantify the behavioral phenotype we often observe in mice due to our experiments. Just recently, the box was finished and put into use, and now it’s time to test and verify its efficacy.

When we look at mice behavior in the lab, we typically use an algorithm like 3-Dimensional Aligned Neural Network for Computational Ethology (DANNCE), which is more robust than traditional techniques because by using machine learning, it can create a virtual diagram of a mouse using points in space and analyze how those points move about over time.

DANCCE Algorithm at Work from Dunn, T.W., Marshall, J.D., Severson, K.S. et al. Geometric deep learning enables 3D kinematic profiling across species and environments. Nat Methods 18, 564–573 (2021).

This gives us a more refined way to quantify mouse behaviors like grooming and turning associated with Parkinson’s disease, the lab’s ultimate focus.

Our experiment consists of testing two variables, drug dosage and the circadian rhythm, on mice behavior, locomotion specifically. By using a technique called Principal Component Analysis, we will take the data of mice moving in 3-dimensions and compress it onto a single image from which we can see differences in mice locomotion. With further analysis, we hope to be able to show that our box does indeed pick up on the differences, no matter how subtle, between mice behaviors in a quantitative and informative way.


Diving into the Realm of Quantum Simulation

     Nanoparticles, quantum mechanics, molecular dynamics, supercomputers, and machine learning. All five of these topics sound like things that Tony Stark and Bruce Banner work on in their free time. However, with modern advances in computing technology these fields are actually able to exist and coexist in a beautiful way giving rise to the real-life field of nanomedicine. 

   I’m coming into the Reker lab as a rising sophomore BME student still trying to figure out what I actually want to study. My interests are spread over multiple disciplines, and it’s hard to pin down exactly one thing that I like. Growing up I loved playing with computers. Not building them like Jimmy Neutron, but simply playing video games like Minecraft. I loved how the computer was able to generate an environment that had similar rules to reality. You have objects in the world, collision rules, like when you jump on slime blocks, gravity, and a day-night cycle. Each of these parts of the simulation combine in a unique way to create the “world” and give a fun experience while playing the game. The combining of multiple processes to generate a real-life simulation is basically what Dr. Reker and other computational chemists are doing with Molecular Dynamics.        

 Before the B-SURF program I had no idea that computational chemistry even existed. After reading through some papers and meeting with Dr. Reker and my mentor Zilu, I’ve learned that computational chemistry could revolutionize the field of drug development. Through simulating interactions of molecules with the Molecular Dynamics software, we’re able to predict what the resulting body would be if we combined the reactants in real life. Specifically, I’m going to spend my Summer researching the potential formation of nanoparticle complexes between different drug and excipient molecules. While most of the chemistry is flying a bit over my head, I hope that as the Summer goes on, and as I finally get around to taking Organic Chemistry, I will understand more about the chemical details of why and how our simulations of molecules form. I’m also excited to learn more about optimizing the parameters of the simulation to perform more accurate predictions. For now though, I’m happy with this past week’s work and my little knowledge in how to generate simple simulations. I might just be a big nerd, but I find it magical that we’re able to take a simple string of letters and pass through a coding pipeline and out comes a visual model of molecules interacting with each other.

     While I don’t get to go to an in-person lab like my fellow B-SURFer’s, I wouldn’t want to change anything about my experience so far. I’m a learn-by-doing kind of guy, and the flexibility of working in a computational lab fits that perfectly. I also know that as time goes on, and as Dr. Reker’s lab gets established in the new engineering building, we’ll eventually get to translate our simulations into real-life. Overall, I’m very excited for what the future holds, and am extremely grateful for Dr. Reker and Zilu for giving me the chance to study underneath them. Here’s to the start of a great summer!

Here is one of my first simulations. In this example, I simulated the interactions between the anti-cancer drug Sorafenib and Cholic Acid. I’m still working on finding the best way to make a movie to upload, so stay tuned for more cool gifs.



Microglia May be My Favorite Cells, but Astrocytes are a Close Second

This week during our morning meetings, each person in this year’s BSURF cohort gave an 8ish minute presentation about their research project, called a Chalk Talk. It is what it sounds like – no prepared visuals other than those you can draw on the board, making what you say and how you say it even more instrumental in the coherence of the talk. Hearing about everyone’s research was super cool, and one that stuck out to me was by Sophie, who spoke about her work relating to astrocytes and the CTNND2 gene.

This summer Sophie is working as part of the Eroglu lab, which does similar work to Staci Bilbo’s lab, which I am a part of this summer. So, it was really cool to hear about a peer diving in to a similar field of research. In her talk, Sophie stressed the importance of astrocyte cells: the most abundant glial cells in the mammalian brain as being critical regulators of brain development and physiology through their interactions with synapses and neuronal communication. Microglia (which I am looking in to this summer) and astrocytes are often considered together as instrumental cells in the brain for immune function and synapse regulation. As she has mentioned in her previous blog posts, Sophie is working with the CTNND2 gene and its role in production of the delta-catenin protein. Previously thought to exist only in neurons, this protein has recently been identified in astrocytes as well! This is really interesting, and poses the question of how alterations in this gene, and subsequently this protein, affect astrocyte cell adherence and general function.

I thought Sophie’s talk was very well structured: she spoke clearly, eloquently and her visuals (of astrocytes, her knock down CTNND2 paradigm, and synapses) were clearly well thought out. Because her research is so closely related to mine, I’m especially interested in the results of her work and the relation of CTNND2 in the ACC, a region of the brain heavily implicated in autism, and the brain focus of my project. The world of neurogenetics has taken us both by storm, working our brain’s to figure out how our brains work.



Science smells like blue cheese?

I can’t remember how many times Dr. G said, “Your first experiment is going to fail,” at our first two meetings.  These words went right over my head, and I definitely didn’t understand what he was talking about until Wednesday, when I was finally allowed to do something in lab by myself.  After two full days of following my postdoc around and being shown so many new techniques my head was spinning, I was told to repeat the first procedure I was shown, creation of a culture medium for E. coli.  Equal parts excited and terrified, I marched off to the cell growth room, dumped 37.5 g of agar in six flasks, added 1.5 liters of water, and autoclaved them.  I was proud that I successfully navigated the autoclave, a huge, intimidating machine that generates a lot of heat.  An hour later, when I removed my flasks from the autoclave, I noticed they were a funny color and producing bubbles.  Hmmmmm.  I asked my postdoc about it, but he thought everything was fine.  The next morning, I came back to a huge mess.  The flasks, which should have contained a light brown liquid, were cloudy and full of clumps of agar.  My postdoc quickly realized my error: I had used LB agar rather than LB broth.  Both bottles are stored in the same cabinet and filled with powder of the same consistency, color, and smell, and I had picked the wrong one.  Uh oh.  Now I had created a huge mess and couldn’t grow the cells from the preculture I had prepared.  All was not lost, however, because I borrowed some media from another lab member.  Long story short, the E. coli I placed in the borrowed media grew too slowly at first and then so quickly that they became overgrown and had to be bleached.  My first experiment had failed before I even got past the first and easiest step.

This early failure revealed a lot about what lab work is like.  First, I’m going to make many, many mistakes.  I’m incredibly fortunate to have a really kind and understanding postdoc.  His patience with my endless questions and general cluelessness about everything in the lab amazes me, and I could not appreciate it more.  As long as I learn from these mistakes, they’re not time wasted.  I can promise you that I will never, ever use LB agar instead of LB broth again.  Second, science doesn’t always work in real life like it does in the textbook.  Sometimes bacteria won’t grow for hours and then multiply too rapidly for reasons unknown to us.  Sometimes you’re working with a “fussy” protein that doesn’t behave the way it should.  Sometimes a protocol that has worked 50 times in a row fails.  There’s a lot more trial and error involved than I was expecting, but again, I’m lucky to be working with a very patient postdoc who has created well-tested procedures.

Two of my goals for the summer are to learn from my mistakes and embrace the uncertainties and questions that accompany research.  I also want to be patient with myself.  I have learned an insane amount of techniques and procedures in the past week, and I forget the details almost immediately after I learn them.  It will take me at least two or three tries (probably many more) before I feel really confident doing something, and that’s okay.  Finally, I want to get to the point where I can walk into the cell growth room without feeling knocked off my feet by the overwhelming stench of bacteria, something that smells to me like bad blue cheese.  All of these goals will be accomplished with increasing hours spent in the lab, and I am ready to have an exciting, surprising, educational, and stinky research experience!


Start of Something New!

I am so excited that I was able to squeeze a High School Musical reference in and even more excited to be starting my BSURF journey with the Sanders Lab. I can already tell from the first week back in Durham that this will be an amazing, challenging, and very hot summer filled with many new people, learning experiences, and good memories. I have very high expectations for this summer and for myself.

First and foremost, I want to learn as much as I possibly can in the next 8 weeks. I have never worked in a research lab before so I have a lot to learn. I have already started to learn about cell culture technique, DC protein assays, LCL protein extraction and western blots, things I had never even heard of a week ago. Using all of these techniques constantly to work on my research project, I hope to improve my lab skills. I have also been doing a lot of research about Parkinson’s Disease and the particular gene I am working with. The research out there is so interesting and rather overwhelming. It is obvious that so many good people are trying to figure out the causes of this debilitating disease to hopefully find a cure one day and I am glad to help.

I have also been learning from my mentors and my peers in the lab about the life of a researcher and about their path to this research in particular. On my very first day I think I got a good overview of the research process. There were some people handling brains, others working in the cell culture room, some reorganizing the laboratory, one working on a presentation of her work for a lab meeting, and everyone running through the halls celebrating when they got news that their grant had been chosen for review. I have also been learning about all of my coworkers, their education, their goals, and on a personal level. They’re really amazing people and I love working and joking with them.

Finally, I want to learn from and about my peers at BSURF. Even though all Duke students are amazing, it seems like the people at BSURF are some of the best. I am already enjoying getting to know everyone and making new friends. I am sure we will bond throughout the summer, whether it’s in our kitchens struggling to cook, in the lounge binge-watching the best of Netflix, and jumping into the pool immediately after climbing the 3 minute walk up swift avenue.

I am so excited to be here and to finally start BSURF. I know that I will learn a lot and have fun doing it. Here are a few pictures of my first time splitting cells by myself! What the HEK 293 cells?



More Bike Rides to Come!

This summer really flew by! I must say I’m so thankful we got this opportunity to get immersed in research! Spending a full day at the lab Monday through Friday really helped me see the daily lives of my PI and post-doc. I learned what it looked like to be a scientist and made a couple of friends along the way!

I’m so thankful for  everyone in my lab who showed me the ropes of the lab! My mentor Megan was really informative at the lab bench and beyond in giving helpful advice!  I’m also so appreciative of the time Dr. D’Alessio put in to make me comfortable at his lab. Luckily I get to continue in this lab during the school year so I didn’t have to say goodbye!

My mentor Megan Capozzi!

My PI, Dr. David D’Alessio!


I really appreciate the time and effort Dr. Grunwald and Jason put to make this summer possible! BSURF allowed for an immersive research opportunity that I wouldn’t be able to engage in elsewhere.