Tag Archives: RF2022-Week5

The innate immune system is highly complex with its intricate maps of signaling pathways and hard-to-remember, long protein names. It’s quite remarkable that this large network can detect pathogens, initiate a number of intracellular processes, and signal for a coordinated body-wide response. Lauren’s project in the Horner lab is particularly exciting because drawing a fuller picture of the RIG-I pathway would help us better understand how the innate immune system responds to an invasion of RNA viruses.  Lauren dived into a lot of the molecular biology details and did an amazing job of explaining her experimental design. More specifically, She’s testing whether 14-3-3e binds to the LIR motifs of RIG-I. Her project involves making plasmids that contain mutated versions of RIG-I, transfecting a RIG-I KO cell line with the plasmids, and seeing if there are changes in binding and downstream functions. After covering the relevant background information and giving an overview of the project, Lauren discussed the specific lab techniques she will be using, such as western blot and co-ip. Lauren not only demonstrated a great depth of knowledge of the system she’s studying but also gave a great explanation of the step-by-step approach of her methods. Studying pathways in the immune system has implications in infectious disease as well as rheumatology, and I look forward to seeing what Lauren will add to the important but incomplete map of the RIG-I pathway.

Over this past week I really enjoyed listening to everyone’s chalk talks and learning about their projects. I was particularly interested in Piper’s talk and her project on the gut microbiome. Nutrition is very important to me, so I’m always eager to learn more about the interaction of our nutrition, the immune system, and the gut.

Piper works in Dr. Lawrence David’s lab and her project revolves around the question: How does total parenteral nutrition (TPN) affect gut fiber fermentation? TPN is a form of nutrient delivery from a tube that is commonly used for patients undergoing HSCT, a stem cell chemotherapy treatment for cancer. TPN is necessary because HSCT can cause nausea and negative side effects which make it difficult to eat. One big downside to TPN is that the nutrients never reach the gut, and the gut microbiome is starved. Piper is looking to explore the negative effects of TPN on the gut, specifically fiber. Piper’s lab has previously established the importance of fiber for gut health, specifically the amount of bacteria and level of diversity. 

Piper did an amazing job of explaining the background information that was necessary to understand her research question. Throughout her entire presentation, she kept the whole audience engaged, and it was easy to follow the logic of her project and methods. Piper emphasized the significance of her project in relation to the issues TPN causes and how her work could open the door for research on less harmful solutions. Of course, her research also has the potential to further what scientists know about the gut microbiome. Overall, I was very impressed by Piper’s chalk talk and I’m excited to see how her project progresses!

Technically spelled DANNCE for 3-Dimensional Aligned Neural Network for Computational Ethology, I found Shivam’s presentation on his work this summer very interesting. This DANNCE contraption is essentially a special box that his lab has been developing to better track mice’s movements during behavior tests. It is a more accurate way to quantify their behavior rather than relying solely on human judgement since it uses machine learning to make visual diagrams of the mice while running the tests. Even though Shivam mentioned that it had been developed to observe mouse behaviors associated with Parkinson’s disease—which is what his lab is studying—when testing them after receiving a dose of a certain drug, I thought it was relevant to my own research at the Ji lab since we do a lot of our own types of behavior tests on mice. Maybe this box could also be a valuable addition in our lab later down the line and I know it would definitely be of great use for many other labs doing similar work. 

Last week’s chalk talks presented a valuable opportunity for all 0f us to learn about the science we are contributing to as individuals and as a group. One such talk was Vidita’s discussion on the potential role of POSTN in ovarian cancer cells’ sensitivity to chemotherapy. She began her talk with an explanation of the stages to ovarian cancer diagnosis and treatment, including the diagnosis of the tumor, treatment using platinum-based chemotherapy, and remission. For the purposes of her and her lab’s research, this also included recurrence of the tumor, tumor resistance to the platinum-based chemotherapy, and progression of the cancer. In order to gain a better understanding of the factors involved in this tumor recurrence and resistance to chemotherapy, her research focuses on the tumor microenvironment – specifically, how the presence of POSTN in the tumor microenvironment affects the chemosensitivity of ovarian tumors. This microenvironment consists of non-tumor cells, extracellular matrix, and blood vessels. In humans, the POSTN gene encodes the periostin protein, which functions as a ligand to support the adhesion and migration of epithelial cells (or cells that line major cavities of the body). It has been reported that large amounts of periostin are found in the microenvironment of recurring tumors, which lends support to the hypothesis that this protein does indeed contribute to chemotherapy resistance in cancerous cells by supporting the progression of the cancer.

I appreciated that Vidita began with a brief description of the motives underlying  her lab’s research, namely the interrogation of the role of the tumor microenvironment in ovarian tumor recurrence. She also did a good job of incorporating and explaining terminology that would perhaps be unfamiliar to a general audience. It would be interesting to see what the next step would be for these findings, particular in terms of treatments and application to other cancers.

Over the course of the past week, everyone presented and explained the research they’ve been doing this summer via a chalk talk. It was awesome to see not only the diverse array of topics and subject matter on the edge of science that everyone’s researching, but also how passionate everyone was about what they’re doing.

I was particularly interested in Rena’s talk on bugs as bioindicators. Although it doesn’t pertain to my research, my mentor before the summer started, Vardhman Kumar, did a project where he created a self healing soft robotic dragonfly named “DraBot” that also works to act as an indicator of environmental status. I thought that was a super awesome project, and Rena’s research felt like its predecessor, and perhaps some of her or her labs results may help develop the DraBot further.

I thought Rena’s presentation was comprehensive and her diagram of the river made her talk really easy to follow. I appreciated how she went one by one through the different locations and explained the implications of their environmental and urban surroundings and how that plays into her research. By framing her whole talk through the diagram, I was easily able to associate her hypothesis and methods with her overall question.

She also made her research seem super compelling by connecting it to broad topics like climate change and pollution which put her whole project into perspective. I think even a complete layperson would find her project interesting because she compares it to real-world issues and how they apply to her potential results. Overall, I was a big fan of her presentation and how simply she was able to put it.

This week, we finally got to hear what everyone in the program has been up to for the last month and I’m impressed. There is such a diverse array of subjects, questions, and techniques we as a program have become involved with and I can tell how excited many of my peers are about their work.

I want to talk a bit about Natalia’s work with neuropathy at the Ji lab. I found her presentation to be informative, clear, and exciting. Natalia also happens to be working just 2 floors above me in MSRBIII, and it’s great to now understand what she’s doing after we happen to get on the same elevator heading to work. It’s also cool that one building can host so many diverse research projects: from studying mouse pain receptors to human gut bacteria and everything in between.

What especially intrigued me in Natalia’s chalk talk was the idea of sexual dimorphism. To recognize that a common and accepted method of chronic pain treatment in male mice just *doesn’t work* for female mice is fascinating to me. I also wonder- in the specific lens of neuropathy- is one sex more susceptible? And do other treatments work only on females because of divergent receptors/neurons? I know that anatomy and physiology of different sexes are divergent but I would have thought something like pain and response to pain/pain treatment would be consistent for all mice as opposed to obviously sexually dimorphic systems like the reproductive or endocrine systems. Many studies only use one sex in mice. Understanding Animal Research says 80% of drug studies only use male mice and other types of studies show the same trend (https://www.understandinganimalresearch.org.uk/news/why-we-need-female-mice-in-drug-

trials#:~:text=About%2080%25%20of%20rodent%20drug,diffe

rently%20in%20men%20and%20women). How much does this leave out of the picture? Fields dealing with sex chromosome inheritance or mating behavior shouldn’t be the only ones considering gender in their studies of mice, flies, and even human subjects (in fact, especially human subjects as they are often the final destination for our findings). This would help understand disease and biology on a deeper level, as we know many conditions (not just genetic ones) present differently in men and women.

I also appreciated this talk because it very clearly suggested the implications for the work at hand on a broad scale; Natalia detailed the significance of her (and the lab’s) work through the narrative of the opioid epidemic and finding better treatments for chronic pain. This really helped me answer the question “why care?” which is a key component in science communication. Natalia, like the rest of B-SURF, did a great job relaying her science despite only having recently discovered her specific project.

I will be discussing about Natalia’s chalk talk about chronic pain in mice. Essentially, Natalia talked about translational pain medicine in terms of short-term and chronic pain alike. The idea of chronic pain is interesting because while pain should be survival mechanism to alert the body of any issues, chronic pain does not serve this purpose accurately and can instead cause neuropathy and/or nerve damage.

It was really interesting to see that there would be a sexual dimorphism in treating the stem cells from bone marrow of male and female mice. The first time I heard about bone marrow was in high school, and while I am not absolutely certain of the research or its procedures, I remember seeing a study on bone marrow cells potentially being converted as sperm cells for reproductive purposes. Again, I am not sure of this accuracy or any relevancy to Natalia’s project, the uses for bone marrow are intriguing to me.

I also liked that Natalia broke down and defined a lot of her terms, such as “immunohistochemistry”  defining it into three parts as antibodies, tissues, and reaction. In this way, it was easier to follow what she was discussing, and I found her chalk talk very informative and applicable.