Author Archives: Shannon Houser

Opportunity and Community…Thanks BSURF!

This has been a truly amazing summer and an experience I will never forget. I was not expecting to love my lab and the research as much as I do. I was also not expecting to meet so many amazing young scientists and have one of the best summers of my life. It was truly a privilege to be a part of such an amazing program, to be trained by some of the best and brightest, and to be a part of such a tightknit (and better than Huang) community.

When I joined the Sanders lab I knew very little about Parkinson’s Disease and how the mitochondria could possibly play a role in the most common neurodegenerative movement disorder. Now, I know so much about LRRK2 and how the mitochondria can effect the cell in so many different ways. Even though I feel like I know so much, I am excited to keep learning and understanding the science behind the disease in the upcoming fall semester and hopefully for many to come.

I really emjoyed being in lab this semester. I was scared that research would make science feel like a job and would take away my passion for it. In reality, I loved going to lab everyday and I was sad to leave. I was lucky enough to be in a very supportive environment where everyone would help me not only with the physical parts of doing science but also with the deeper understanding. I am very thankful to everyone in the Sanders lab for teaching me so much about the world of science. They taught me to always ask questions, to question my work just as much as the literature, and that communication with other scientists was essential.

At first, I didn’t know why it was important to understand exactly what every reagant or technique we used did. Now, I am so thankful for the small quizzes on what PIC does or where the DNA went in my protein samples. Teaching me about every small step helped me understand the process at large so much better. I believe in the future this knowledge will help me figure out where I made a mistake or maybe even guide my project in new directions.

I am also so thankful for BSURF for providing me this amazing opportunity. I have learned so much in such a short amount of time about research, communicating science, and what the future might hold. The poster session and the lunch was so generous and it was so amazing to see everybody succeed in their labs. If it wasn’t for BSURF I would not have met my amazing peers who I hope to have by my side for the next three years at Duke. We had some amazing times, whether it was at the food truck festival, in the eno, eating in downtown, or simply hanging out at Swift. I’ll miss BSURF, my lab, and my new friends but I’m glad to say I’ll see them all in the fall.

Final Poster Session!

Pro Tips and Proteasomes

Over the past seven weeks, we have heard from some of the most amazing professors at Duke. We have not only heard about their groundbreaking research, but also about their personal lives and their path to success. Among all those great stories, Dr. Gustavo Silva’s stuck out to me the most.

Dr. Silva is a very young professor at Duke. He was born and studied biology, both as an undergraduate and in graduate school, in Brazil. He only moved to the United States for his post-doctorate. I was intrigued by Dr. Silva’s accent, youth, and his research.

Dr. Silva studies the ubiquitin proteasome system which marks specific proteins for degradation within the cell. He started his presentation by explaining how oxidative stress can cause molecular damage, which leads to a decline in physiology and the onset of disease, something I have become quite familiar with while studying Parkinson’s these last few weeks.

He has found that ubiquitination and proteasomes are sensitive to too much cellular stress. Dr. Silva has also discovered that there are many different ubiquitin chains that are used to signal proteins for several different alterations, not only cell death. For example, ubiquitination and proteasomes are used to modify ribosomes where tRNA binds, and thus are vital for translation.

One of the most important lessons that Dr. Silva taught us had nothing to do with biology at all. He taught us to dream big and to follow our hearts. He believed that we could do anything we wanted if we put our minds to it. He also encouraged us to look around us at all the amazing peers, professors, and resources we have at Duke. He believes that building a strong support system and large community will help enable us in the future and will inspire us to be the best we can be. Lastly, he told us to make sure we have good mentors who have our best interests at heart.

I am thankful to the BSURF program for providing so many amazing speakers. I have thoroughly enjoyed learning about their research, their past, their failures, and their success.


Parkinson’s Disease is a common neurodegenerative disease characterized by the death of dopaminergic neurons, which can be caused by oxidative stress in the mitochondria and subsequent DNA damage. It is known that the mutated variant of the LRRK2 gene causes Parkinson’s Disease; however, the role of the unmutated gene, outside of its kinase activity, is relatively unknown. We seek to determine the role of the unmutated LRRK2 gene under oxidative stress and DNA damage by simulating these conditions with toxins in both wild type and CRISPR edited LRRK2-KO cell lines. We will be using western blots to measure the differences in phosphorylated proteins known to respond to DNA damage and different levels of cyclins and related proteins that may contribute to the cessation of the cell cycle. We expect to find that the resistance to DNA damage and the percent of cell death is different in the two cell lines. We also expect to find that the LRRK2-KO cell line, under stressful conditions, creates a checkpoint in the cell cycle that stops growth and division. Understanding LRRK2’s role and its pathways can help us better understand how the increased kinase activity of the mutated gene causes Parkinson’s Disease.

All in a Day’s Work

“Choose a job you love, and you will never have to work a day in your life.” ~Confucious

I truly love the work that I do and the people I work with. I am so lucky that my days are not only filled with cells and amazing science, but laughter and heartfelt conversations as well.

As far as the science goes, cells and protein take up much of my time. Every other morning I need to split cells and change their media so they stay alive and happy. Often, after I split my cells I plate them so that I can do treatments on them the next day. The most important part of cell culture is aseptic technique. I have to make sure that I do not contaminate my cells in any way. Since I have two different lines, it is very important that I keep them separate.

Another very important part of my day that is often overlooked is the math. I have to make sure that I plate the right amount of cells and media so that both of my lines are at the same confluency to ensure that the most variables are controlled for. I do this by counting the cells and making sure to plate an equal number in each well. I also have to use math to make sure I have an equal amount of protein in each gel well and to make sure I use the correct amount of antibodies.

Throughout my day I follow many different protocols and use a lot of different equipment. I have learned how to do DC protein assays, to do Western blots, to collect protein, to do treatments, and to analyze my gels. When I am not working, my lab is always talking and laughing together. We have plans to go to baseball games, make dinner, and to go to a Young the Giant concert. Some of us have even been on 8 hour car rides back home! I have had a great time in my lab, both with the science and my coworkers.

Reduce, Reuse, Reinvent mutant plastic eating bacteria

Everyone had amazing chalk talks and I feel like I learned so much! This week, I especially enjoyed Ella’s chalk talk on making mutant enzymes that can degrade plastic. Although I am fascinated with the brain and the molecular biology that is being used to combat its diseases, Ella’s project caught my attention by addressing something bigger than ourselves and just as pertinent to our survival, the Earth.

At first, Ella really grabbed my attention with the estimate that by 2050 there will be more plastic in the ocean than fish. In high school I learned about the Great Pacific Garbage Patch and other horrible pollutants in the water, but this prediction really put the problem in perspective, and frankly scared me. She then explained about the bacterium that can break down PET, which is found in all single-use water bottles. I was amazed that this bacterium even existed and how it had evolved to digest just what we need it to. Sadly, the enzyme that helps break down the plastic is not very effective right now, and that is where Ella’s project comes in.

Ella is using error prone PCR in order to make many different mutant versions of the enzyme PETase. I was blown away. I think using a machine that purposely makes errors in the enzymes DNA to create mutations to hopefully make this protein more effective is absolutely ingenious. She then would ligate the DNA into plasmids, transform the plasmids into E. coli, and test the bacteria’s ability to break down and survive on plastic effectively.

I also thought that Ella’s pictures of PCR and of the growth of the transformed E. coli made it much easier to understand than it otherwise would have been. Everything was well labeled, her protein pathways were easy to understand, and her talk flowed really nicely. I like how she connected it back to the big picture throughout her talk. For instance, in the middle of her talk she explained that the bacteria create a by product that can be used to create anti-freeze and will make cleaning up the oceans and using these bacteria economically enticing. Sadly, many people need a financial incentive in order to do the right thing. I really enjoyed this week and learning about everyone’s research.

My PI was almost Zion…but now she’s cooler!

Dr. Sanders is an amazing mentor and I have truly enjoyed getting to know more about her and her incredible research during these last three weeks. I first met Dr. Laurie Sanders when she gave a talk to the SPIRE Fellows program. I enjoyed her talk and was fascinated by her research and that is why I asked to work with her and her lab this summer, and hopefully for the next few years. You can read more about Dr. Sanders, her research, and her vast accomplishments here.

When Dr. Sanders was in high school, she desperately wanted to be a Duke basketball player. She was sadly unable to fulfill this dream because of an injury. She then continued her education at Cornell, where she fell in love with science. When she was about to graduate, one of her advisors told Dr. Sanders that her (very good) GPA would not be enough to get her into medical school. Because of this poor mentorship, Dr. Sanders is now a mentor for many undergraduates at Duke (like those in the SPIRE program) and believes that good mentorship and a solid support system are some of the most important factors in the undergraduate experience and beyond.

Dr. Sanders then went to the University of Buffalo, where she received her PhD in biochemistry and met her husband. She completed her post-doc at The University of Pittsburgh at the Pittsburgh Institute for Neurodegenerative Disease. This was where she started “thinking of the disease from a new and original angle, bringing innovation to the field” of Parkinson’s research, which she sees as her greatest accomplishment in her career. She has received the first Parkinson’s Action Network Postdoctoral Advocacy Prize and was also rewarded the William N. & Bernice E. Bumpas Foundation Innovation award. She works extensively with mitochondrial damage, repair, and dysfunction and its role in Parkinson’s Disease. Her colleagues commend her on her risky but extremely rewarding ideas that continue to advance our understanding of the most common neurodegenerative disease in the country.

Lucky for me and the future of science, Dr. Sanders eventually returned to her dream school and now works in the Bryan Research building with her amazing lab team. They continue to study the role of mitochondrial DNA damage in Parkinson’s Disease models in vitro. Outside of her remarkable discoveries, Dr. Sanders’ time and passion lies in her children. Dr. Sanders has three boys and is truly outnumbered at home. She loves that they keep her busy and she knows that balancing her ever advancing career and her growing boys will be her favorite challenge. Dr. Sanders had the potential to be a Duke basketball star, but her name will still go down in history (and on many published papers) and she has the potential to help millions. I’m certainly a fan!

LRRK2: What are you up to?

On my very first day my amazing PI, Dr. Sanders, handed me a sheet of paper with three goals for this summer. I was very surprised that I was able to start working on my first goal, learning mammalian cell culture and proper aseptic technique that same day. Today, I am incredibly happy to say that I have completed that first goal. I have worked with a line of human embryonic kidney cells (HEK293). I can now successfully and independently (much to my mentor’s delight) split, count, thaw, make media for, and collect protein from these cells.

I will be using my mammalian cell culture techniques throughout the rest of the summer in an effort to meet my two other goals and to answer important scientific questions. One of my goals is to determine if HEK293 cells lacking a  LRRK2 gene are more sensitive to environmental toxicants and DNA damaging agents. To do this, I am planning to treat wild type cells with LRRK2 and cells that have had the LRRK2 gene removed with the same doses of certain toxicants and DNA damage inducing agents and analyze the differences. Some of the many common toxicants I am planning to use are rotenone, hydrogen peroxide, and mitomycin C. If I am able to complete this project and get promising results (fingers crossed), I can move on to my third and final goal.

My last goal is to determine whether LRRK2 deficiency leads to cell cycle checkpoints in the presence or absence of the same environmental and DNA damaging agents that were used to determine cell viability before. I will be checking the levels of unique proteins associated with different parts of the cell cycle to see if the checkpoints are working properly. I will be using DC protein assays and Western Blots in order to carry out these goals, as well as my mammalian cell culture technique to keep my cells happy throughout.

Why is this my project? My lab, the Sanders lab, has discovered the importance of mitochondrial DNA damage in neurons affected in Parkinson’s disease. The LRRK2 gene is known to be a genetically significant factor for the onset of Parkinson’s disease. Although scientists know that it plays a role in many Parkinson’s patients, they do not fully understand what it does. My lab believes that LRRK2 may play a crucial role in the mitochondrial DNA damage they found earlier and may play a critical role in the cell cycle when such DNA damage (produced by the exposures in vitro) is present. This is why I am looking at both cell viability and cell cycle checkpoints in HEK 293 cells with the LRRK2 gene and the same cells without the LRRK2 gene. We hope to understand this gene better, so we can understand how it is affecting Parkinson’s patients and to try and find a way to reverse the damage it does.


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?