Thursday, July 30, 2015

What I Did This Summer: Lab Experiences

From the looks of my posts this summer, it would not look like I was at a Biology REU. In fact, it looks more like I was in a psychological/theological study performed within the context of a cellular biology lab.

So now that my summer is coming to a close, I will give you Dear Readers the highlight reel. And if that is too long, there is a TLDR (too long didn't read) version at the bottom.

Week 1
Back Corners and Extroverts Do Not Mix

On the first day of bench work, I was given a two hour background lecture on the experiment, and then I was shown my desk. For the next four days I sat in that little corner, scared out of my mind, and staying nearly silent. The other undergraduate in the lab and I only exchanged maybe a total of seven sentences a day. My voice was broken by the end of the day solely because I did not use it nearly as much as I usually do.

I was miserable and homesick. The only lab work I did was make a few restriction maps of the sequence I needed to make a construct of a lysosome membrane protein called LAMP1 (lysosome associated membrane protein 1). We needed one with a red fluorescent tag, and that was going to be my job.

Even though I came up with a plan, I was too scared to talk to the people in my lab about it. Nothing was accomplished that week.

Life Lesson: Don't be afraid to be yourself and actually talk to people. Otherwise you're going to be miserable and sit alone.

Week 2
Learning the Little Things

Week two was when I finally started to work. The other undergrad asked me on that Monday if I was going to do anything, to which I shrugged and turned back to reading another journal article so he wouldn't see the angry tears on the corners of my eyes. Then he stood up and grabbed a bunch of beakers with water and labeled them like they were the materials used to subculture cells. We spent the morning with a culturing tutorial.

The rest of the week was spent learning other little tasks in the lab from my PI's wife and the graduate student. I learned how to increase the concentration of DNA so I could have it sequenced and I received my own cell line to maintain. We even started some steps for my own project. All of the techniques I learned that week were used for the rest of the summer, and my failures resulted from me forgetting what had happened.

Life Lesson: Appreciate the little things, because they some day become the big things.

Week 3
Scientists Get in to Fights

It took a while, but I finally started to get to work on my own plasmid on my own cell line. That meant that I got to observe proteins under the Live Cell Imaging microscope. Up until that I point I had been pretty anxious to get started, but I finally started to feel like I was not a dead weight in the lab. Most of my days were spent getting help from the grad student and then reading in the corner. I did not feel as homesick.

As my cells continued to grow, I grew more comfortable in my lab. I still did not talk to very many of them outside of the graduate student, but I did not mind all too much. That is until a meeting for NPC (the disease that I am researching) research came to Notre Dame.

At the meeting, the presenters got in to arguments and some even left the room in a huff. Being an undergraduate who had just gotten in to the field, I knew very little. So I sat next to the other undergraduate and laughed at the whole thing.

Life Lesson: Scientists are normal human beings, but they really need some more humility. That includes myself.

Week 4
Community Building

Over that weekend, I ran in to the Post Doc from China after Mass. We talked for a while. Instead of talking about Science, we talked about our families and the importance of love in the household. She was very impressed with my maturity and diligence. We became friends. Not only did I not feel like a dead weight, but I felt like a companion to the other lab members. My confidence increased.

At this point, I actually got to talk to the other undergraduate more often and Dr. Vaughan came by every day to just talk to us about whatever he found amusing that day. Considering how much time I spent sitting and waiting for the next thing to happen, it was nice to have some variation in my day.

All of the social interaction helped me come back to being who I am, a happy and confident woman. This was super helpful because it was at this point that I started to work on my own more often, and it was when I did not need super detailed protocols in front of me to be successful. I give a lot of credit to the people in my lab for that.

Life Lesson: You cannot work in isolation.


Week 5

Science is 90% Failure but the 10% makes it worth it

Because my cells were still growing, I did not have a lot of work to do on that Monday. The other undergrad also did not have a lot to do. So I ended up procrastinating by cleaning up my back corner. Let's just say the Vaughan lab has a lot of packrats.

My transfections were not very good, and I forgot how to run an agarose gel. My homesickness started to return as my failures returned over and over again. To defeat it, I spent more time working outside of the lab, reading literature on methodology and dedicated myself to the task I believe God made me for.

Then it started to work. My PI was happy. My lab members and I were friends. Life was good.

Life Lesson: You have to know sadness to truly understand joy.


Week 6
First Week Alone...but not really alone.

During this week, I started to cotransfect my red protein with our green mutant proteins. We wanted to see if the mutants were degraded like many of the other members of the field proposed, or if they were in the lysosome like we hypothesized. Unfortunately, I could not keep my cells healthy, and I could not find any of my proteins as I needed to.

So we killed my line and I stole some from the graduate student. He had kept some cells on the side just in case someone (me) had a problem with their cell line. Even though I was working more independently, I was never completely alone. That's what I love about science. No matter how hard you try, you can never be completely on your own.

Here is a great example: The other undergrad was on vacation, so I was alone in the back corner room. I told my fellow REU students that I would be pretty lonely during that week. They actually came to visit me!

Oh, and I got bored being in this old back room, so I did this.



Life Lesson: The longer you sit around trying to do a task on your day only wastes more time. Also, inside jokes are fun.

Week 7
Learning What Failing Looks Like

This had to be my lowest point in the program. At the very beginning of the week, it looked like everything was working again. I thought that my cells looked good, and my restriction digest had been proven correct once before.

Over and over again my digest failed. Then my cells died.

And I cried.

Failure was not something I wanted to experience with only three weeks left in my program. I needed data and I needed to have something to show for all of the work I had done this summer. Personal growth certainly was not something I could put on a graduate school application.

But I learned that it was more important to have faith that things will work out, and I learned that I did not have to feel completely alone in the struggle. My coworkers made me smile and they made sure that I was doing the right things so that I could be successful in the future. Even though I had very little to show from this week, I believe this was the point where I truly became a scientist.

Life Lesson: You will fail, but you do not have to go through it alone.


Week 8
Experiencing Community

Because I was back to square one (sort of) on the first half of my project, I had a lot of free time to work on other things. I spent most of my free time trying to clone a sequence in to the vector we wanted, and I failed to do so for the most part.

The rest of the time I spent time talking to my fellow lab workers. I got to see the dark room, and I watched the others work on their experiments. While none of these things really made a huge contribution to my own work, I learned a lot. And since the NSF wants REU students to learn as much as possible, I would like to think I was successful.

I talked to my cells like they were my children as I looked at them under the microscope, and on Thursday I got to see what they looked like.

They were all dead again.

Because Thursday was technically my last day of work for that week, I would not let myself be defeated by this moment. I pulled out my older cells and I split them for a new experiment. Dr. Vaughan did not really want me to keep trying.

I had to. So I did.

AND I GOT SOME PICTURES.

Life Lesson: Sometimes the most exciting things come out of the most unexpected places.

Week 9
Like Week 1 All Over Again

Because I had very little going on, and because my PI was out of town, I spent the majority of the week sitting behind my desk and working on stuff on my computer. On top of that, I hardly spoke a word to anyone in the lab until Wednesday afternoon. Apparently they thought I was painfully shy and scared to talk.

I prepared to make my experiments work for the last time. I was anxious to say the least, but I was very excited to see if I could get the results that my PI wanted to see so badly. On the day of my imaging, I sent out various texts for prayers and tweeted specifically for people to pray for me using a Hail Mary (Catholics) or The Lord's Prayer (Protestants). Then I proceeded to bless my coverslips and my microscope.

And hey look! I got a picture or two!

Life Lesson: Prayer and patience can get you anywhere.


Week 10
Wrapping Things Up

As the REU came to a close. I spent the majority of my time in the imaging room editing the pictures I made of my cells. Since the microscope was off, it was pretty cold, but that was ok. I realized just how much I was going to miss everyone in my lab, and I actually felt pretty bad about hiding away in the back room working.

My PI gave me a lot of advice on how to deliver my talk, and then I spent the rest of my time just working on perfecting my talk and enjoying my last few days in the lab. This included celebrating some of my fellow undergrad's accomplishments and chatting with the Post Doc.

On Thursday, my last day of lab, I killed off the rest of my cells and called it a summer.

And then I made this post before I give my talk tomorrow.

I can't believe I am done.

TLDR
Week 1: I did nothing and was a scared little child.
Week 2: The other undergraduate helped me get out of the corner and I learned really basic stuff.
Week 3: Scientists got in to a fight
Week 4: I imaged stuff and made friends
Week 5: My results actually started to work out
Week 6: I leave funny notes and get annoyed when stuff doesn't work.
Week 7: My cells all died and I cried about life, but my coworkers are nice people.
Week 8: I failed a second time, but I came back and got pictures
Week 9: My last experiment was stressing me out and it took a week to happen
Week 10: I felt like I did nothing, and then I left.

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