Alicia Arnold

Finding Natalie: A Summer Spent with Zebrafish

My first experience with scientific research happened when I was an 11th grader in high school. At the time, my school did not offer an advanced biology class but I wanted to learn more than what the general course offered. Fortunately, my Biology teacher was also the advisor to the Environmental Club and wanted someone to take on the task of gathering data on our local stream ecology. She agreed to let me earn credit for the class by completing an independent research project as long as I could pass the course assessments. This ignited a passion for field research and was instrumental in my later decision to pursue fisheries science in college.  

Unfortunately, somewhere along the way, I convinced myself that I was not suited, or “smart enough” for the research or academic life and instead pursued a project management and data analysis path instead. Eventually, I became a teacher in order to return to science and share my love of learning with students. However, it wasn’t until I participated in the SEP summer teacher professional development program in 2015 that I received training on biotechnology techniques and felt confident about teaching them to students. I also had my first one-week experience in a Fred Hutch research lab and that left me wanting more. The benefits I have seen in sharing the biotechnology curriculum developed by SEP with my students convinced me to apply for the Hutch Teacher Fellowship. I am excited to share my experience with my students!

At the start of the summer, there was so much to learn about and I admit that at times I felt overwhelmed. But in just eight short weeks, I am amazed that I can now explain most of what is happening in the above figure. In the figure above, steps A-C had taken place almost a year ago and it was from this particular data set that my project developed. After a quick tutorial on the basics of working with zebrafish and the lab equipment, I was trained on how to do the RNA in situ hybridization (ISH) process [3]. Remember the concepts of Central Dogma or Transcription & Translation from Biology class [4]? This process utilized these genetic mechanisms to identify where a specific gene is being expressed and is used in many different areas of research on many different organisms. In brief, I treated samples of preserved embryos with mRNA probes tagged with digoxigenin (DIG). Next, an antibody for DIG is added followed by a colorizing molecule that ultimately allows us to see where the mRNA is expressed in the embryo at that particular stage of development. The stain appears purple in the images below. A secondary antibody staining process was then performed to identify all of the cranial motor neurons expressing a specific protein tagged with green fluorescent protein (GFP) [5]. This is the brown stain in the image below. The hope is that where the two stains overlap will confirm gene expression specific to different areas of the vagus and show how vagal axons grow over time to their targets. 

It took several tries for me to get the ISH process down, and I made mistakes along the way.  But unlike experiments in the classroom, I was able to reflect on the process and make improvements for the next round. It reminded me that we need to have better discussions in the classroom. I would like my students to understand that when experiments don’t have the expected results, you can still learn something from them. 

In addition to working with established probes, Austin and I identified 15 new gene candidates from the 2022 data set and shared these with Dr. Moens. Austin then narrowed the list down to 9 genes to design primers in order to make the RNA probes. It felt like I was helping complete a complicated puzzle, and it was exciting to think that some of the genes we identified might prove useful in completing the final picture.  

What also surprised me during my time in the lab is how often the researchers will add in additional variables to test just to make sure they are getting the best results they can. For example, with one ISH round, I tested whether using a pre-frozen solution worked as well as one that was freshly prepared, or if parts of the ISH process were affecting the GFP staining process. If something didn't work as expected, we didn’t just throw our hands up in the air.  Instead, we thought about why and what could be done differently. This was a big takeaway that I want to share with my students, since so often they are used to doing labs with an expected result and not much time is spent on the reasons behind asking their own questions and designing their own experiments. This is something I hope to change next year and will be one of the goals of my curriculum project.

In addition, because my research project is built on the foundational concepts around protein synthesis, I would like to create a curriculum that utilizes SEP’s “Flow of Genetic Information” and “Amino Acid Starter” modeling kits. Students will use these models to gain a deeper understanding of how this process is linked to various diseases such as cancer.  

I will also have the opportunity to house an aquarium of zebrafish in the classroom. Students will be able to observe many biological concepts such as: carrying capacity and abiotic/biotic interdependencies, cycling of nutrients such as carbon and nitrogen, and development and cell specialization. I also hope to include a Socratic seminar style lesson to have students explore the controversy around using animals in biomedical research.  

Mostly, I am excited to share the experience of being in a lab doing research on a daily basis with my students. Even soft skills such as taking notes, following lab safety rules, and working as part of a team have all been reinforced as important lessons for students to experience. This has been a summer of finding my joy again in science, and I hope that I will inspire students to find joy in making their own discoveries.  

I would like to give a special thanks to Dr. Austin Seroka for his patience and guidance in mentoring me this summer, to Dr. Cecilia Moens for her time and willingness to provide me with this amazing opportunity, to the rest of the Moens lab staff for all their help, and finally to Natalie, the zebrafish without this work would be impossible.