Week 3: Welcome to New York

I arrived in New York City! I’m happy I got to meet the Bostrom Lab in person after seeing them in Skype meetings for several months.

After a bit of time getting my IDs and paperwork in order, I was able to start with some lab work. I was introduced to an ongoing project that I will be helping out with this summer. The project is focused on understanding how alterations in the gut microbiome may affect osteointegration in joint replacement implants when an infectious agent is introduced. The gut microbiome is the community of bacteria that lives within the intestines. The gut microbiome is highly involved with digestion, but more and more we are seeing that the gut microbiome has a profound impact on the whole organism. We are particularly interested in how the gut microbiome affects bone growth and immunity because this is important for bone growth around an implant and resistance to infection after implantation. The gut microbiome can vary greatly between individuals, and ultimately we would like to know if there are ways we can alter a person’s gut microbiome that will produce better outcomes for joint replacement.

RNA sequencing is one method we are using to quantify the response of the joint to the implant, infection, and microbiome status. This week I got some training and helped out with the preparation of some RNA samples for a quality check. RNA sequencing gives an idea of what genes are being expressed in a tissue.  Instead of looking at a whole genome sequence like I did last week, this only focuses on the RNA that are currently being transcribed. The genomic data tells you everything about the organism, but the RNA data tells you what is happening in that tissue specifically at that time point. RNA expression varies between tissues such as cortical bone, cancellous bone, and bone marrow, so it is important to carefully separate those samples. I learned that is can be difficult to get clean separation, and the process involves many cleaning steps with buffer solutions.

One of my favorite things I got to see this week was a mouse model for joint replacement. They designed a tiny titanium implant, and the surgeons in this lab perform a miniature total knee replacement on the mice. It’s really impressive to see the precision that have to perform this microsurgery. I appreciate how well they are mimicking a human total knee replacement; it makes the model translational and relevant. In the coming weeks, I may even get to assist on some of the mouse surgeries.