Vivian Sun :: Week 1 :: A Motley of Beginnings
Week One of my time at Johns Hopkins University got off to an interesting start on Monday, June 19! My Airbnb is within walking distance of JHU's East Baltimore (hospital and medical school) campus, so I began my first full day in Baltimore with a brisk (albeit warm) walk to the Volunteer Services Office to pick up my official volunteer ID. I left early to make sure that I had sufficient time to get my badge and make it to my lab before 9, even with any directional difficulties! I later got to Ross Research Building, where my lab is located, ten minutes before 9 and met my fellow lab members. Katie, an undergraduate student from Muhlenberg College who is also a summer intern like me, was the first person I met. She introduced me to Monica, the lab manager and technician, as well as to Paul, a postdoc at JHU. The fourth-year JHU grad student I would be working with, Snow, came in a bit later, as did HeeSun, another fourth-year JHU grad student. I met my PI, Dr. Daniela Cihakova, shortly after, who greeted me warmly and welcomed me to the lab. She asked me briefly about my immunology background and how much I knew about the immune system so that she could gauge my abilities and know where I should begin to familiarize myself and prepare for the internship. This whole week was a bit different because Autoimmunity Day was right in the middle of it (more on that in Day Three!) so everything would be a bit mixed up, but next week I'll likely be more focused on one theme (Snow's project!). This week being my first week, it was more of a general overview of how the lab works and of what I'll be doing during my time here.
My first day, I watched Paul make an emulsion for mice injection as Snow finalized something in the animal room; I also filled out some paperwork to be cleared to work with the animals. Later on, I accompanied Snow to the animal room in the basement of a nearby building to watch her check on her mice cages and separate any mice (to prevent overcrowding if they had new litters of pups), as well as to perform general maintenance with the animals. I learned how to sex the mice and how to approximate the ages of the mice based on their size, the amount of hair they have, if their eyes are fully open or not, etc. I also watched and learned from Snow the proper protocol to work with mice (sanitizing the hood, working wet, etc.). It is crucial for the mice to avoid infection since the mice she uses are Rag2 gamma chain double knockout mice, meaning that they lack both B- and T-cells and innate lymphoid cells - they're extremely immunodeficient. The animal room is called a room, but is actually the entire basement of a nearby building. It houses over 30,000 cages of mice and rats, usually with 1-3 rats per cage and 6 adult mice per cage to prevent overcrowding (size limitations are different if pups are born). It had a distinct, pungent smell, but I got used to it after a few minutes.
On my second day, I sorted antibodies with Snow in preparation for the next step of her project. These antibodies are markers that are mixed with fluorescent dye, essentially, that will help identify certain cells when the cells are analyzed using flow cytometry. Flow cytometry is a widely-used technique, especially in this innate immunology lab. The gist of it is that cells are lined up, one by one, and suspended in a liquid; lasers are shot at them and they're excited until they emit a wavelength of light. This wavelength of light can be used to analyze the properties of these cells. Snow's project focuses on studying the effects of monocytes and macrophages, the innate immune system, on myocarditis and its progression to dilated cardiomyopathy. The next day was Autoimmunity Day, an annual event (similar to a conference), organized by Dr. Cihakova and Monica, with many guest speakers to discuss autoimmunity and see different projects within the field, all with the theme of autoimmunity. As such, I read some review articles and primary literature written by the speakers at the event to prepare! I also looked at the histopathologies of stained mice and human hearts on slides under a microscope with Snow. I learned how to assess the level of cell infiltration in the heart on a scale of 1-5, just as they do in their lab's papers.
Autoimmunity Day was the third day, so I spent all day at the conference and listened to various guest speakers discuss and present their current research projects and findings. The topics ranged from innate lymphoid cells and their effect on autoimmunity and tolerance, to microbiota and the eye, to inflammation inhibiting the endogenous remyelination in multiple sclerosis, among others. The discussions were rather detailed and summarized long-term projects in just 30 min or an hour; as such, it was a bit hard for me to follow at times, especially with all the unfamiliar and highly specific immunology jargon, but the topics were very interesting! There was also a contest for the best abstract for a paper in progress; HeeSun won first place and Paul won second place, but all participants were invited to present their posters with the general outlines of their projects (similar to EXP night come fall term next year, where we'll stand by large posters and talk about our summer EXPeriences). All in all, I was glad to have been lucky enough to coincidentally come to the lab in time to attend Autoimmunity Day.
The fourth day for me started out with animal training! It was a two-hour affair, but I was able to learn the procedures for working with mice - I was even able to pick up a mouse! It was a bit difficult since the black mice in general (one of which I picked up) tend to be more aggressive/more likely to bite, but it turned out okay. Afterward, I did a lot of running around Baltimore that muggy morning to get my animal training forms signed and stamped so that I could be cleared to work with the mice later. I was a little annoyed at having had to waste much of my time running around and waiting in offices for certificates or signatures, but it will all be worth it when I am able to begin handling mice and help Snow out with her project! I went out for lunch with my lab members to a local farmer's market that takes place every Thursday and met with Dr. Cihakova to discuss Autoimmunity Day. She asked me more about general immunology and helped me understand each lecture as well.
Every Friday begins with a lab meeting. Dr. Cihakova usually begins them with a quick summary of a recent scientific paper she read the past week, and we go around the table and introduce the articles we each read over the past week as well. Sometimes these lead to long discussions and others, depending on the interest of each person at the table in the topic of the paper, may just be a quick 2-3 minute summary of the article. Afterward, one lab member will present their current research findings and where they are in their projects; all are free to provide advice and suggestions to them as well. A fun quirk my lab has is that cakes are brought in every once in a while. This lab meeting was one of those days! HeeSun was presenting on her research - the role of innate lymphoid cells in pericarditis - and she brought in a very cute Opera Cake from a nearby, much-loved French bakery called Patisserie Poupon. After the lab meeting ended, I met with Snow and she explained to me how to analyze the results of flow cytometry using a program called FlowJo. She showed me how to "gate" the graphs, which basically entails selecting a portion of the graph's data and allowing the user to focus on that part in particular. This gating process can be repeated multiple times to choose the data wanted. In general, flow cytometry graphs are divided into four subsections, just as if you split the first quadrant graph into four different sections. The position of the data point and the labels of the x and y-axes could determine if that point, in particular, was positive or negative for the x- or y-axis label (this label usually being an antibody specific to a certain type of cell). If the data point was positive for that antibody, it would mean that the cell expressed that antibody, and if it were negative for the axis label, the cell did not express that antibody; this analysis would be repeated for both the x- and y-axes. You would need to choose the label's antibody carefully, but the cell could be identified by using the antibodies' identifying properties. I also learned about another one of Snow's projects (a side project) and in greater detail about her main project (mentioned before) and her current findings therein. She even gave me Cap'n T Cell, a cute plushie of a T-cell - it has small receptors on its head!
Looking ahead, I'll be working with Snow on Monday to prepare for her experiment on Tuesday, in which she will sacrifice six mice and harvest their hearts for analysis with flow cytometry. Stay tuned for next week's update! :)
My first day, I watched Paul make an emulsion for mice injection as Snow finalized something in the animal room; I also filled out some paperwork to be cleared to work with the animals. Later on, I accompanied Snow to the animal room in the basement of a nearby building to watch her check on her mice cages and separate any mice (to prevent overcrowding if they had new litters of pups), as well as to perform general maintenance with the animals. I learned how to sex the mice and how to approximate the ages of the mice based on their size, the amount of hair they have, if their eyes are fully open or not, etc. I also watched and learned from Snow the proper protocol to work with mice (sanitizing the hood, working wet, etc.). It is crucial for the mice to avoid infection since the mice she uses are Rag2 gamma chain double knockout mice, meaning that they lack both B- and T-cells and innate lymphoid cells - they're extremely immunodeficient. The animal room is called a room, but is actually the entire basement of a nearby building. It houses over 30,000 cages of mice and rats, usually with 1-3 rats per cage and 6 adult mice per cage to prevent overcrowding (size limitations are different if pups are born). It had a distinct, pungent smell, but I got used to it after a few minutes.
a cage of mice with food
On my second day, I sorted antibodies with Snow in preparation for the next step of her project. These antibodies are markers that are mixed with fluorescent dye, essentially, that will help identify certain cells when the cells are analyzed using flow cytometry. Flow cytometry is a widely-used technique, especially in this innate immunology lab. The gist of it is that cells are lined up, one by one, and suspended in a liquid; lasers are shot at them and they're excited until they emit a wavelength of light. This wavelength of light can be used to analyze the properties of these cells. Snow's project focuses on studying the effects of monocytes and macrophages, the innate immune system, on myocarditis and its progression to dilated cardiomyopathy. The next day was Autoimmunity Day, an annual event (similar to a conference), organized by Dr. Cihakova and Monica, with many guest speakers to discuss autoimmunity and see different projects within the field, all with the theme of autoimmunity. As such, I read some review articles and primary literature written by the speakers at the event to prepare! I also looked at the histopathologies of stained mice and human hearts on slides under a microscope with Snow. I learned how to assess the level of cell infiltration in the heart on a scale of 1-5, just as they do in their lab's papers.
Autoimmunity Day was the third day, so I spent all day at the conference and listened to various guest speakers discuss and present their current research projects and findings. The topics ranged from innate lymphoid cells and their effect on autoimmunity and tolerance, to microbiota and the eye, to inflammation inhibiting the endogenous remyelination in multiple sclerosis, among others. The discussions were rather detailed and summarized long-term projects in just 30 min or an hour; as such, it was a bit hard for me to follow at times, especially with all the unfamiliar and highly specific immunology jargon, but the topics were very interesting! There was also a contest for the best abstract for a paper in progress; HeeSun won first place and Paul won second place, but all participants were invited to present their posters with the general outlines of their projects (similar to EXP night come fall term next year, where we'll stand by large posters and talk about our summer EXPeriences). All in all, I was glad to have been lucky enough to coincidentally come to the lab in time to attend Autoimmunity Day.
a poster advertising the schedule for Autoimmunity Day
The fourth day for me started out with animal training! It was a two-hour affair, but I was able to learn the procedures for working with mice - I was even able to pick up a mouse! It was a bit difficult since the black mice in general (one of which I picked up) tend to be more aggressive/more likely to bite, but it turned out okay. Afterward, I did a lot of running around Baltimore that muggy morning to get my animal training forms signed and stamped so that I could be cleared to work with the mice later. I was a little annoyed at having had to waste much of my time running around and waiting in offices for certificates or signatures, but it will all be worth it when I am able to begin handling mice and help Snow out with her project! I went out for lunch with my lab members to a local farmer's market that takes place every Thursday and met with Dr. Cihakova to discuss Autoimmunity Day. She asked me more about general immunology and helped me understand each lecture as well.
the famous Johns Hopkins dome, just across the street from the farmer's market!
Every Friday begins with a lab meeting. Dr. Cihakova usually begins them with a quick summary of a recent scientific paper she read the past week, and we go around the table and introduce the articles we each read over the past week as well. Sometimes these lead to long discussions and others, depending on the interest of each person at the table in the topic of the paper, may just be a quick 2-3 minute summary of the article. Afterward, one lab member will present their current research findings and where they are in their projects; all are free to provide advice and suggestions to them as well. A fun quirk my lab has is that cakes are brought in every once in a while. This lab meeting was one of those days! HeeSun was presenting on her research - the role of innate lymphoid cells in pericarditis - and she brought in a very cute Opera Cake from a nearby, much-loved French bakery called Patisserie Poupon. After the lab meeting ended, I met with Snow and she explained to me how to analyze the results of flow cytometry using a program called FlowJo. She showed me how to "gate" the graphs, which basically entails selecting a portion of the graph's data and allowing the user to focus on that part in particular. This gating process can be repeated multiple times to choose the data wanted. In general, flow cytometry graphs are divided into four subsections, just as if you split the first quadrant graph into four different sections. The position of the data point and the labels of the x and y-axes could determine if that point, in particular, was positive or negative for the x- or y-axis label (this label usually being an antibody specific to a certain type of cell). If the data point was positive for that antibody, it would mean that the cell expressed that antibody, and if it were negative for the axis label, the cell did not express that antibody; this analysis would be repeated for both the x- and y-axes. You would need to choose the label's antibody carefully, but the cell could be identified by using the antibodies' identifying properties. I also learned about another one of Snow's projects (a side project) and in greater detail about her main project (mentioned before) and her current findings therein. She even gave me Cap'n T Cell, a cute plushie of a T-cell - it has small receptors on its head!
Cap'n T-Cell, to the rescue!
Looking ahead, I'll be working with Snow on Monday to prepare for her experiment on Tuesday, in which she will sacrifice six mice and harvest their hearts for analysis with flow cytometry. Stay tuned for next week's update! :)
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