Tag Archives: RF2022-Week4

Down a few stairs of the LSRC and through the doors of the Center for Cognitive Neuroscience lies the Pearson Lab. As I walk in each morning, I’m greeted by the other undergrad in the lab, Chris, my mentor Dr. Anne Draelos, and whoever else is there. To start my day, I set up my laptop with a monitor and get settled into my desk, usually with tea or coffee in hand. Anne always comes by to check in on the progress I’ve made with my project, and we discuss objectives for the day as well as general goals going forward.

The bulk of my day consists of coding, debugging, and researching. Currently, I’m working on creating plots that have live updates as new neural data comes in and also including information about the stimuli that’s present during the experiment. Tackling tasks like this requires me to explore different Python packages and experiment with different lines of code. As a coder, my best friends are Stack Overflow and Slack. Whenever I get stuck working on a piece of code, my first line of defense is to google to the problem and then look on Stack Overflow for solutions from people with similar problems. If I’m still stuck after a couple of attempts, I’ll use Slack to send a message to Anne. Slack is one of the main forms of communication at the Pearson Lab, aside from talking in-person. We all use Slack to send messages about meetings, questions, and other general lab information. My mentor Anne works between two labs, so at least once a day I hear “If anything comes up, send me a message on Slack,” and her response comes minutes and usually seconds later.

As for general day to day life in the lab, many other people trickle in throughout the day. There can be as many as 10 or 15 people there on a given day. My desk is in the side room, along with Chris, Liz (another one of my mentors on the improv team), and Trevor. The PI, Dr. John Pearson, comes down from his office around once a day and checks in on everyone. We have lab meetings on Mondays, a meeting with the improv team on Thursdays, and a meeting to merge code branches on GitHub on Fridays. I really enjoy the comradery of the lab and the research work I’m doing makes me feel like a real computer scientist!

For me, it’s kind of hard to write about a day in my life at the lab because of how varied the days have been from the very beginning. However, this isn’t a bad thing. It’s kept every day looking more like an adventure with many things to learn from rather than getting monotonous and boring. Typically, I do go in at the same time—10:45 a.m., after our BSURF meetings in the mornings on Tuesdays, Wednesdays and Thursdays—except on Mondays when I go in until after lunch because we have lab meetings from 9 to 11 (ish) and Fridays when I go in at around 10 am. Going into MSRB III in the morning, all the way up to the 6th floor  has become my favorite thing, especially getting to my little desk area within the lab that has an amazing view of the Duke Chapel. Usually at least one of my two mentors will be there already, so I greet them as I set up my area with my computer and notebook.  

Since we just recently solidified the plans for what my project for the summer would consist of, we’ve been going through the steps that we have planned out and seeing which would be the best to perform next or continue whatever was not finished the previous day. Lately this has included lots of immunohistochemistry to stain mouse DRG’s for analysis under a microscope and this past Friday and Saturday I learned how to do RNAscope as well for this project. Both are relatively long procedures that involve lots of waiting time between steps in the protocol, so I have been making use of that time by reading. It had been a long time since I was able to do that peacefully because of how packed my days are usually during the school year so I’m very much making the most out of it. At some point in time, usually between 12:30 and 1:30, I take a little lunch break where I appreciate having some time to spend with other lab members since everyone is usually very engrossed in their own work all day. Afterwards once I am done with whatever I had planned to do for the day I check with my mentors one last time if there is anything else they want me to do, observe, or help themA day in my life at the Ji lab  with before heading out, which has usually been between 5 and 6:30 depending on the day. Although some days I come out more tired than others, I am always eager to go back the next day for more activities within the Ji Lab.  

A morning in the lab usually starts with me going over past protocols and adjusting amounts/volumes of reagent based on experimental conditions and optimization guidelines. Most of what I have done during the past weeks was subcloning plasmids that had been designed during the first week. Depending on where I am in the process, a day in the lab could be filled with procedures like enzyme digestion, purification, ligation, or transformation. When I wait for a reaction to run to completion, I would read about the immune system, Yersinia pestis, or some primary literature that connects the two. I would also have time to discuss the scientific background and questions with my mentor almost everyday. This is something I enjoy a lot because it allows me to see the bigger picture of the work I’m doing. In the afternoon, in addition to the things I mentioned above, I would also observe how my mentor does some of her experiments, and I would practice cell culture techniques that aren’t used in cloning. This is important because after I create the plasmid coding for the mutant proteins, I will need to transfect human cells and infect them with Yersinia pestis. Every Tuesday, I meet with my PI to go over results, troubleshoot, and discuss future steps. Also on Tuesdays, during lab meetings, I learn about the projects that other researchers in the lab are working on.

What I particularly enjoy about doing research during the summer is that the science is the only thing I worry about. Doing research during the school year means that I would need to set up an experiment, go to class, and then run back to the lab to end the reaction and set up for the next step. The process is very hectic. As my PI told me when I first joined the lab, “science is better when you have time to think about it”. I’ve frequently found myself coming up with ideas while taking walks during lunch breaks.

Whether it’s a BSURF morning or not, it wouldn’t be a day at the lab without me starting off by investigating a new route to MSRB1 in my unending pursuit of the fastest way to the lab. After I get there, I’ll usually settle for a couple of minutes before I get started, because one of the perks of the lab is almost entirely unbounded hours. You can come when you want and work when you can, all we want as a lab is progress and results. As Dr. Grunwald always says, science doesn’t take breaks and I think the Varghese Lab’s standards fit that philosophy perfectly.

Many days of the week there are lab meetings or subgroup meetings where we’ll meet with Dr. Varghese and discuss our various projects. Typically I can’t contribute much, but despite this, I’m still afforded the opportunity to observe scientific discussion at the highest level. After these, I’ll get started on whatever tasks I have for the day. This often varies a lot; I may spend the whole day planning and reading papers, I might be working on building microfluidic devices to use in future experiments, or I could be working on cell culture. In addition to all of this, I occasionally get to do some imaging work or observe cell seeding into the microfluidic devices, a process more complex than it seems. I lot of this happens under a Biosafety Cabinet Hood, a machine that basically makes sure the inside of it stays super sterile. I have to be super careful with cells, reagents, media, and everything else that I work with because maintaining sterility is super important in ensuring both your cells stay alive, and that your experimental results are valid.

In the upcoming weeks, my days will probably change because many new materials are coming in so I’ll be able to make some new advancements in my project. The number of things I’m going to learn by the end of the summer is way beyond what I expected and I can’t help but be excited for the upcoming weeks.

Every morning I arrive at the Soderling Lab with an idea of what my goals and steps are for the day ahead. At some point within the past week, my bench mentor and I would have discussed the experiments, protocols, and concepts I would be working with, as well as any questions I might have had for him. Still, if I am unsure about where to start, I only have to ask and thus be on my way.

Some days, this means starting off in the cell culture room, beginning a days-long protocol for transfecting some NIH3T3/Cas9 cells underneath the HEK cell hood. Or, I might be observing my handiwork from days prior with the microscope, ensuring the cells look healthy. At my station, I may be gathering reagents to run a PCR, or gathering a marker, my epitubes of purified DNA, a 10uL pipette, and some TE Buffer to measure DNA concentration on the 3rd floor of the Nanaline Duke building. I might find myself in the laser room to observe the results of my immunofluorescent staining from a day or so ago, imaging my samples and preparing to quantify the cells I can see. This leads to me practicing my Excel skills in order to evaluate the consequent data, creating graphs and running statistical tests. There are also the occasions on which I visit the “mouse house”, or GSRBII, where I suit up in PPE and get to see in vitro experiments become in vivo ones, or where I attend in-house lectures and presentations by grad students and visiting scholars.

Some days, I am running one experiment after another only to realize that it already past 4pm. Others, I am performing a single task that requires my attention the entirety of the day. Regardless, I have learned something new and check in with my mentor about what’s next before heading out for the day.

A day in the life of a microbiome scientist:

My day at the David lab consists of a lot of sample processing. Human fecal samples don’t just automatically go through a machine and become pretty strings of As, Ts, Cs, and Gs or numbers explaining their exact molecular makeup. Instead, I spend a few hours before lunch cycling through a series of steps including: adding various buffers to the samples, spinning them down, filtering them, incubating them, and transferring between many small tubes that had to be labeled earlier, and then spinning and transferring some more. In previous weeks, I was preparing samples for a machine called the HPAE which measures carbohydrate content, but this week, with my mentor out with our familiar foe Covid, I have been helping another lab mate do DNA extraction for his research. It can be a bit tedious, but after having practiced the process a few times this week I’ve become exceedingly more efficient and independent during the process, and can now perform a whole extraction myself. It’s also been an opportunity to talk to my lab members as we load and run samples almost out of muscle memory.

We then break for lunch, my favorite part of the day. Yes, I love food (especially the free food provided for lab meetings and other lab events!), but I also love getting to know my lab members. Most of us eat lunch together every day around the same time- something I’ve really come to appreciate as I get to know each of them better. They’re all exceptionally welcoming and helpful, as well as just really nice people to have random conversations with over Panda Express. After lunch, I finish up the rest of the processing and store the samples in the fridge to use later.

In the off time between sample spinning or when it’s too late to start a new batch of DNA extractions toward the end of the day, I hunker down at my desk and begin learning R. Because: what happens after all of these meticulously prepared samples go through their respective machine runs? That’s where data analysis comes in. While I have little experience with the software, many PhD students in the David lab are adept at using R to visualize and analyze data.

I follow online tutorials, resources provided by my lab mates, and use practice data files to play around with the software and figure out how to plot biological data. I’ve attached my earliest and proudest creations from such a session, but I’ve learned a lot since and hope to continue learning both wet lab and computational techniques moving forward.

A day in my lab typically starts off with sitting in front of a microscope. I put in my earbuds to listen to music that keeps me in the zone. I put on gloves and prepare to inspect a sample from a local creek in Durham underneath the microscope: counting, measuring, and identifying insects. I take my lunch break after I get to a good stopping point (ideally when I have worked my way through a sample), and afterwards, I pick up where I left off and continue to count my insects, recording data in an Excel spreadsheet throughout.

Other days include field work, waking up in the early hours to beat the Durham summer heat to set up traps or collect water samples in the creeks nearby. I really enjoy these mornings (other than the number of mosquito bites I receive) because I get to spend some time in the field, out and about and collecting data that I will later get to analyze and learn about in the lab itself later on.

I check in with my mentor every day, giving progress reports, showing him my findings, and collaborating with him in identifying insects and figuring out logistics of my BSURF summer project. Some days, he also takes me to the river center or the environmental engineering building to help with some lab work or to observe different kinds of machinery in the other buildings.

My lab also has weekly meetings, where we identify our goals for the week and address our goals from previous weeks as well. I get to hear about other scientists’ research during these meetings and meet new people pretty regularly, so I really enjoy sitting and absorbing the information that is offered to me through these meetings. Overall, I thoroughly enjoy my lab work, as it is work that I feel relaxed about and enjoy.