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.

My Summer in Song Lyrics

Being stuck in a lab all summer has taught me one thing: Music is very important.

Ok. I learned a lot more than that, but my Spotify playlists got me through the hardest times, the happiest times, and the quietest times that I have experienced in the lab.

So in honor of that...I am going to post the lyrics that I feel encompassed most of my "feels" this summer!

Ben Rector's "The Beat"

And then the beat comes

And then she's moving on the dance floor

And I wonder what she's running from

I had just left Nashville, and I felt like I was running from the story I did not think I should have to tell anymore. I found myself dancing around to this song everywhere, and I actually found myself smiling by the end of my first week of lab.

Keith Urban "Days Go By"

Yeah it's all we've been given,

So you better start livin' right now

'Cause days go by,

The first week was miserable and it felt like I was never going to get out of my basement lab because I chose fear over everything else. Once I started to live a little and enjoy myself, the weeks started to fly by. This song was my theme song for my Saturday Solo Dance Parties. I still can't believe that I am about to leave this place.

Kacey Musgraves "Dime Store Cowgirl"

You can take me out of the country

But you can't take the country out of me

As odd as it seemed to everyone around me, I fought to keep my southern identity while in this new place. Cowboy boots were not just functional, but they were a statement. I also used the word "y'all" significantly more than usual. I missed home, but I knew that it was never too far from my heart.

Matt Maher "Adoration" 

Jesus, Lamb of God, saving love for all

Lord of heav'n and Earth

I bow to You, bow to You, I bow to You

I was very anxious when I had to run experiments that I had never seen before. I also failed too many times to count. When I felt down on myself or life in general, I would play this song on repeat for hours. It was as if every moment I spent listening to it, regardless of what I was doing at the time, was a prayer. I felt so at peace with this song in my ears and the Lord on my heart.

Young the Giant "Cough Syrup"

If I could find a way to see this straight

I'd run away

To some fortune that I, I should have found by now

I hate to say it, but at many points, I considered hiding away because I did not feel like I was reaching my potential. Either that or I thought that I was not doing what God wanted me to. I couldn't see straight. Thankfully I figured it all out.

Jake Miller "First Flight Home"

I can't predict the weather

But you should know that I

I'll be on the first flight home

1. Indiana Weather Sucks.
2. This was my spin song, and there really is no deep purpose. It's just awesome.

Dan and Shay "Party Girl"

Take me to the party girl in the same t-shirt

that you weart to bed while the ceiling fan turns

to the rhythm that we're spinning bare feet on the floor in the living room light

I at one point got really in to country again when the homesickness settled in. That's when I found Dan and Shay, and this song in particular. Even though I love to dance and be around people, this summer has shown me that chillin' at home is perfectly ok with me.

Beyonce "Flawless"

You wake up, flawless

Duh.

Tenth Avenue North "The Truth is Who You Are"

And it's not enough to just say, "I believe"

'Cause truth is that talk is cheap

So grace give me eyes to see

I had a really great conversation with one of my REU friends as we drove from Chicago to South Bend (or maybe it was the other way around...) about what it truly means to be a follower of Christ. It takes a lot more than just simple words. Faith is life. My faith and my life changed and grew dramatically this summer.

Passion Pit "Take a Walk"

Practice isn't perfect

But the market cuts the loss

I remind myself that times could be much worse

I really like this song, but I had never noticed these lyrics before. It sort of relates to the fact that no matter how many times I tried, I still messed up, but at the end of the day, life could be far worse than having to run a few more trials.

Andy Grammer "Back Home"

And no matter where we go

We always find our way back home

And now I am about ready to return to Nashville, TN. Man I miss my coffee drinking, hipster-filled, southern hometown.

Just Some Gratitude

I am a big fan of saying Thank you to people. I am also a huge fan of writing unnecessarily long letters sharing that gratitude. And while I am still going to do that for my lab, I feel like I should share some silly moments that I am thankful for...

Thank you REU fellows for not thinking I was a complete freak when I opened our first conversation with, "What animal would you ride in to battle?"

Thank you Emma for getting ice cream with me instead of staying up too late at the movies.

Thank you Dr. Vaughan for reminding me of the differences between Amish and Mennonite People

Thank you fellow undergraduate for reminding me why I am glad that I am no longer premed

Thank you Dr. Whaley for literally always bringing food along with you.

Thank you grad student for putting your name on the plates we poured together so they could blame you if they were all contaminated.

Thank you Post Doc for constantly complimenting my pearls.

Thank you NPC meeting for giving me a few good stories to laugh about.

Thank you Morgan for understanding my desperate need to go to coffee shops.

Thank you room 613 for sprouting mold so I was forced to do laundry and pack two weeks before leaving.


Thank you roommate for letting me go to bed at 9pm and wake you up for the gym at 5:30am.

Thank you to my PI's wife who understood my sass.

Thank you random old people who sat next to me at Mass for holding my hand during the Our Father.

Just watch. This struggle could be so real.

Thank you random grad students for letting me play trivia with y'all even though I contributed essentially nothing.

Thank you Vaughan lab for teaching me that it is OK to not say anything for several hours and that I won't spontaneously combust if I do.

Thank you Darby for taking us in to the Daughters of Saint Paul book store when we went to Chicago.

Thank you grad student for knowing how to troubleshoot every mistake by already having made the same mistake.

Thank you Kevin for walking through my lab weekly and giving me something to give you crap about.

Thank you chemist for existing in the biology lab. You kept me sane.

Thank you to the physics REU kids who always ate my cookies.

Thank you to Hal, my microscope, for not breaking down when I did.

Thank you Netflix for understanding just how exhausted I was in the evenings and sticking with me.

Thank you to Dr. Vaughan for reminding me that sarcasm is arguably the most intelligent form of humor.

Thank you to Notre Dame's Yik Yak for actually being humorous.

Thank you to COS7 cells for being strong enough to deal with my constant abuse.

Thank you to the speakers I found in the back corner that made my Sunday dance parties in the lab that much more enjoyable.

Thank you to South Bend weather for always giving me a reason to change an outfit and only have to wear my rain boots for a couple of hours.

Thank you to the lakes that taught me that geese are not kind creatures.

Thank you to lysosome related proteins for giving me 48 hours of free time every experiment

If you couldn't tell...that really long incubation period is why I had time to write this....oh the life of a cell biologist. You can't get me back to Biochemistry any faster...

Why Comparison is Good

Being a 21 year old who dances, is a science major, and is an active community member are all things that lead to a predisposition to comparison. I would love to say that it is simply my environment that leads me to compare myself to others, but that would not be true.

It's because I am a woman.

Now now, before all of the feminist fighters close the tab, allow me to finish my thought.

The Genius of Motherhood

"In fact, woman has a genius all her own, which is vitally essential to both society and the Church." Pope Saint John Paul II

What is this feminine genius? What makes a woman intelligent in a unique way that is not found in men?

It is empathy and feeling.

Society is highly aware that women are more likely to describe their experiences through feelings. They are more likely to cry in a movie, and they are more likely to have an emotional connection to an experience. While the level of emotion is different for each woman, the fact that women are innately tuned to their emotions is highly important.

But how is this a skill? What makes that genius?

Women are more likely to sense the feelings of others around them. This comes evolutionarily from the development of motherhood. The role of a mother in a person's life shapes who they are. Young men learn to respect women from their fathers and they learn what emotion and hard work look like from their mothers. Young women have a role model for their adulthood constantly in their lives.

Most importantly, mommies are the ones to kiss boo-boos.

They start out as cuts and bruises on the playground, but they develop in to deeper issues from the world around us. Regardless of the nature of the injury, a mother is able to help heal her child. How many times do we attempt to hide our issues from our mothers and how many times do we fail to simply because she could tell something was wrong without a word?

God gave women empathy so that no person would be completely alone.

Because women were designed to become mothers, all women have the same genius ability to take away pains from this world. From childhood, a girl is able to tell when something is wrong, either with their friend or with a stranger.

Where Genius Becomes Idiocy

Sensitivity to the world does not just include emotion. In fact, women are able to see far more. According to a study at Brooklyn College, women can see more shades of color then men.

However, because women are so highly relational, the people around them are far more important than the shade of green they are wearing.

As a woman, I notice everything about the people around me. Their height, their weight, their hair, their clothing, their laugh, and everything that I can use to describe them. It makes remembering a face easy, but it causes many issues down the road.

When sin entered the world, the devil took a permanent perch on a woman's shoulder. He whispers in her ear, telling her that she is not good enough, that she will never be good enough. In a desperate attempt to be worth something, a woman will seek out what is good enough.

She will look at the other girls.

She will see their physical form and think, "She has a much better body than me."

Obviously this is wrong for us to do. People have been harping at magazines for changing the images of their models for years, and self promotion articles often remind girls to stop thinking that someone is better than them. Society believes that the real problem lies in self depreciation rooted in our negative comparisons.

They forgot about the second half of a woman's thoughts.

To make herself feel better, she will look at another girl and think, "Well at least I am prettier than her."

We have grown to make comparison a form of consolation for our insecurities. There is always someone that is better than us, but we can always find someone beneath us. If it is not fitness, then it is intelligence. If it is not either of those things, it is number of friends on Facebook. No one wants to be on the bottom.

Women are able to sense the emotions of others, but because we are so concerned with our own image, we ignore everyone around us. Instead of noticing the unique soul standing before us, we think about the mass of carbon based life and its material success. At the end of the day, we only care how we feel in relation to these earthly things.

Fun fact guys: feelings are not objects.

We are using objects to create our feelings.

Because we are constantly comparing ourselves in a way that tears others down, we are not only distorting our own self image, but we are also beating down on the spirits of those around us. People can tell when you are judging them. And no matter how much we don't want to admit it, the feeling of being judged hurts even more when your comparisons define your life.

So if we are going to use comparisons to define ourselves, then we better be using the right ones.

A Better Comparison

The best way to define oneself is in this way:

"See what love the Father has bestowed on us that we may be called the children of God. Yet so we are." ~1 John 3:1

God made each woman, and He loves them very much. If we are children of the Creator, would it make sense for Him to include something worthless in His family? Of course not. Therefore, we must recognize the truth that each person is beautiful and important and destined for more. There is no way on Earth that any woman could be beneath everyone else, not fundamentally at least.

If we are all on a level playing field, then we must act like we are. The Devil wants to break us apart and make us feel weak by telling us that we are less than what we are, and we perpetuate that sentiment by letting other people know that feeling.

But what if we changed that?

A Call to My Fellow Women

You don't know exactly what someone is insecure about. But as a woman, you can tell that there are insecurities filling her subconscious. You can see her looking around the gym, wondering if she actually fits in with the athletic people. You can see her hiding her exam from her peers, worried that she is not as smart as people thinks she is. You can see her posting solely happy statuses on Facebook and only sharing exciting things, hiding the life that we all have: Netflix marathons and screaming in to pillows.

We need to remind them that they are special.

It doesn't matter how you do it. The easiest way is a simple compliment. Because women are able to see so much more in a person than just their hair color and their height, we can come up with something nice to say to every single person.

One time I told a girl that I adored her hair and that I wish mine looked like hers.

Apparently it was one of her largest insecurities.

You may never know the impact of your single smile or compliment. All you know is that it is important that every person feels special. If you want to be happy, then let everyone else be happy too. I really like the opening verse in "Biscuits" by Kacey Musgraves:

Taking down your neighbor won't take you any higher
I burned my own damn finger poking someone else's fire
I've never gotten taller making someone else feel small
If you ain't got nothing nice to say, don't say nothing at all

If you notice that someone has something that you wish you had, don't try to tear down your neighbor to forget that. Let the girl know that her legs are awesome. Let your lab partner know that you wish you were as good at test taking as they are.

We need to start building people up.

Because once they are confident, then they can starting building us up in return.

Let's fight the devil ladies, one compliment at a time.

Oh. One last thing.

You want to know who is beautiful? Read the first word on this line.

What You Won't Get From My Twitter/Insta

I have been at Notre Dame for seven and a half weeks now, and I just realized that I have not informed my Dear Readers on what I am actually doing here! They say that you do not fully understand something unless you are able to explain it to someone else, so I am going to try that here! (And if I fail...my talk in two weeks is going to be really bad.)

Lysosome Storage Diseases
What does that mean? Basically, your cells take up cholesterol from your diet. Similar to how when we eat and our food travels to our stomach, cholesterol from outside of the cell accumulates in the lysosome.

From there, the cholesterol goes to the Endoplasmic Reticulum to be made in to other things or be sent to different organelles. In lysosome storage diseases (LSD), cholesterol cannot get out of the lysosome. There are many different versions of these disorders, resulting in many different rare diseases.

Neimann Pick Type C (NPC)

In the Vaughan lab, where I have been spending my summer, we are looking at a lysosome storage disease called Neimann Pick Type C (NPC for short). NPC affects the perkinje cells in the brain, and causes dramatic brain damage. Damage to the brain causes several other symptoms that are pretty diverse for each patient. NPC affects about 1 in every 150,000 people.

By people I mean children.

Before the age of ten.

They die before they complete adolescence.

A long time ago there was a famous coach at Notre Dame named Ara Parseghian. His children lived in Tucson, AZ, which is where I grew up. They had four children, and three of them were diagnosed with NPC, and they all passed away.

Because there were no treatments available for these children, their mother set up a foundation named after their grandfather to further research on this rare disease. My lab for this summer is part of the small community of researchers trying to figure out what happens in NPC and how to treat it effectively.

NPC1

The first step was to identify the protein coded by the recessive gene in NPC. They found that most of the mutations affected a protein called NPC1.

To explain that picture up there, there are many parts (domains if you are a scientist) to this protein. The first part that matters are the many sequences that pass through membranes. The next part is a dileucine signal, meaning that the protein goes to the lysosome. Add those two things together and you get a lysosome membrane protein. The last part to pay attention to is the sterol sensing domain (SSD).

What do you get?

A protein in lysosomes that binds to sterols, cholesterol in particular.

If this protein is messed up, then moving cholesterol from the lysosome is not going to work very well is it?

What happens to NPC1?

This is the part that our lab is trying to figure out. Because this is such a young field of research, there is not a lot of information on the mechanisms or pathways. There are two different models that are currently being focused on.

Endoplasmic Reticulum Assisted Degradation

The first hypothesis relating to the effect of mutation on NPC1 was presented by Dan Ory in this paper. In this model, the mutations in NPC1 cause the protein to be folded differently. Most of the time, when a protein is not folded like it should be, then it is broken down before it can move on to other parts of the cell. Because most protein folding and modifications happen at the ER, that is where the mutant protein is recognized and set up to be degraded.

So if the protein that normally binds to cholesterol to be transported is degraded, then you don't have anyone to hold on to cholesterol. If cholesterol is not bound to anything, then it gets stuck in the lysosome. BOOM. Lysosome storage disease.

The key to this theory is that when NPC1 binds to cholesterol, the lysosome sends everything to the ER in little packages called vesicles. NPC1 is in those membranes and travels to the ER again that way.

The Vaughan Model

The lab that I am participating in this summer has a different theory as to why cholesterol is not leaving the lysosome. Before I explain, I will give some background.

There are these things called membrane tubules. Think of long highways that stuff can travel on through the cell. It kind of happens like this (but not exactly):

Before I got to ND, the Vaughan Lab had noticed that these little structures come off of the lysosome. Interestingly, these membrane tubules were not present in mutant cells. Their hypothesis was that cholesterol traveled through the cell via these membrane tubules, and NPC disease happened because the membrane tubules were not present in the mutant cells.

But wait? What does that have to do with NPC1?

That takes another protein.

STARD9
In an attempt to understand the mechanism better, the Vaughan lab looked for other proteins involved in making membrane tubules. What they found was a new motor protein called STARD9. Remember the video above? (if you didn't watch it, this is your chance) STARD9 would be the guy moving everything along essentially.

In healthy cells, they could see that NPC1 and STARD9 were in the same place.

This did not happen in the cells that represent NPC.

Many people say that this happens because of the degradation model that I described above. However, in our microscopy experiments, the Vaughan Lab could see the mutant protein in lysosomes. If they made it to another organelle, then it did not degrade.

Where I Come In
Now if you have been reading this blog post, you probably are wondering what this has to do with me. If you look at my tweets and my instagram posts, you would not get all of that theoretical stuff. I am pretty sure NPC is rarely mentioned...

These are the things that happen in the Vaughan lab...

My job is to help identify lysosomes and then see if I can find the mutant NPC1 protein inside the lysosomes. The parts I need are: glowing proteins, a Live Cell Imaging microscope, and good cells.

Finding Lysosomes with New Stuff
There is another protein that are in lysosomes called LAMP1 (lysosome associated membrane protein 1). Everyone uses it as a "tag" for lysosomes. When I look at cells expressing the genes for this protein along with a florescent tag, I can see it glowing that color under the microscope.

Our lab has a version that glows green. That's fine and all, but all of our mutant proteins glow green. If we wanted to say that our mutants were in the same spot as LAMP1, then we would need it to glow another color.

I am making a red version. Well...cherry.

This involves me cutting up a bunch of DNA and then running it down the gel to get the sequences I want so I can put it together in a new way. The sequences I want have a specific size, and if I cut it properly, then I can see it really well.

If you want to know...it did not work.

Where Oh Where is NPC1?

If you follow me on Twitter or Instagram, this part of the project is probably what you have seen the most. As I said earlier, if you have a tag on a protein, you can see it glowing under the microscope. So I put some of the DNA in my COS7 Cells, wait 48 hours, and then I use our fancy microscope to look for cells with glowing proteins.

I named the microscope Hal. This is Hal and I. We're really tight if you didn't know.

Now there are a few challenges to getting a good picture. When you put these weird plasmids in the cells, they freak out and crank out these proteins all the time, which makes them pretty sick. Also, if you do not properly take care of your cells, they are going to die. I had that experience happen twice. One time it was so bad that this happened...

Well actually I was just an idiot who couldn't keep her cells alive.

Why Does This Matter?

Obviously my contribution to the lab as an undergrad is minimal. However, by using images taken from the microscope, we can do some computations to determine if the mutated NPC1 protein is in the lysosome with LAMP1.

If the numbers are good, then it would be another piece of evidence supporting Dr. Vaughan's model.

And if we have a better understanding of what happens to the mutated protein, then we can study why the membrane tubules are no longer present in the mutant. This can help us understand how cholesterol normally travels through the cell. By finding locations and mechanisms, better treatments for NPC disease (and other related diseases) can be developed.

What Are You Up To Now?

No. That is NOT safe lab practice.

Ok. Lab dance parties are pretty fun, but that is not exactly what is going on (at least not when anyone is watching). Basically I have failed a million and two times, but I am working on improving. I also am learning a lot about what everyone else is doing and how everyone else's experiments work. The Vaughan lab is full of cool people.

Lab Buddy: Read "Other Undergrad who sits in the same back corner room."

Of course that does not necessarily mean that I have learned any extra social skills by being in a basement lab all summer. I am pretty sure I have started to become more of an awkward scientist....

But really, I am thoroughly enjoying my time in the lab. My cells are currently very healthy, and I am getting closer to making my own "glowing protein." Hopefully I will have some valuable results by my REU symposium...

So there. Now you know what I am doing.

The Two Most Difficult Confessions

During my Senior year of high school, I had the opportunity to go to Confession during our Kairos retreat. I was very anxious to confess a sin of mine that I desperately wished to wash clean. Due to negative treatment of my ex boyfriend, I had left God because I did not believe that He could love me. As I tried to come back, I felt the sin of those silent months holding me back.

I wanted to sprint to Christ.

So I confessed my sin.

The priest told me that it wasn't a sin and wrote off my Confession.

I was heartbroken. Did Jesus not wish to forgive me? Was the sin ever going to be washed away? If the priest did not forgive me in personae christae, then did the Confession not count? These questions filled my heart and I dreaded every confession afterwards. Even though I was a good Catholic girl, I hated Confession. It filled my heart with fear and doubt and worry.

But of all the Confessions I have had, there were two that scared me the most. I will share these stories in order to emphasize the importance of Confession in the Christian life, particularly those to a priest in the form of a Sacrament.

SEEK 2015: Round Two

It was the afternoon of our third day at SEEK 2015, a huge conference filled with 10,000 Catholic college students, hundreds of religious, and numerous guest speakers. My friends and I saw that the line for Confession was short (a rarity at a Catholic conference), so we decided to go.

I did not want to be there.

I had gone to Confession not too long before, so I did not have any sins on my mind. The only thing that I could think of was that period of time that I spent without Christ. Even though it had been three years since I had tried to confess that sin before, my heart was still filled with immense anxiety and regret for not recognizing God's love. It was all I had left to Confess.

I felt sick to my stomach.

I could not admit that to a person again.

It was so easy to just talk to God about it in the chapel. I could pretend that He was kindly responding and inspiring me. I could pretend that it was all ok, and the sin was washed away. By devoting my personal prayer to that one transgression, I was able to fake my freedom. The simple fact that I was still praying over this time period three years later proved otherwise.

I had to tell someone who was physically there.

"In failing to confess, Lord, I would only hide You from myself, not myself from You."

--Saint Augustine

In the back corner of the Confession room was a priest in a gray habit. I had never spoken to anyone in his order, so I decided to go to Confession with him. After saying a few venial sins, I let out a shaky breath and admitted my guilt yet again. My voice had cracked in the middle and I was crying. Partially because of my guilt, but mostly because of my fear. What was he going to say this time?

The priest looked at me and answered me as if I had no reason confessing that sin. He told me that if I had confessed it before that it was gone, and I needed to be grateful to God. It was as if Jesus himself was telling me to get over myself.

As I was about to leave, the priest stopped me and pulled a miraculous medal out of his habit. (I still have no idea how he fit the little packet in there. Perhaps I was the only one he gave a medal to.) He told me to remember to pray a Daily Rosary and to stay close to Mary because she would keep me close to Christ. I thanked him and left.

I put the medal on immediately after, and I wear it nearly every day. This medal is a reminder that, unlike the first priest to hear my confession, God will always show mercy. My soul had been cleansed over three years ago, and I could move on with my life.

All I needed to do was admit my fear and come to Christ.

By physically going to Confession, we force ourselves to admit that something needs to change. We cannot hide behind our own thoughts and feelings and imagination. Confession allows us to find His love and mercy in a very personal manner. It is terrifying, but it is of the upmost importance in our lives.

Letting Go

Another one of my larger problems in life is that I don't let go of...anything. Most importantly, I never forgive people for hurting me. If they say something mean, or if they mistreated me, or if they were rude one time, or if they just give me a weird look, I don't let go. My mom likes to remind me of the time I thought a man gave me a mean look from the car next to us when I was seven.

Apparently, I talked about it for the rest of the day.

So imagine how much worse that got by the time people actually hurt me.

I recently have had the misfortune of being hurt by a good friend of mine, and I was harboring a lot of anger. When I prayed, I prayed for God to heal me. I refused to forgive him for what he had done to me. My prayer life was centered around him, much like my life had for the past several months.

My pride told me that I was too good to forgive him for using me.

"A soul does not benefit from the sacrament of confession if it is not humble. Pride keeps it in darkness. The soul neither knows how, nor is it willing, to probe with precision the depths of its own misery. It puts on a mask and avoids everything that might bring it recovery."

--Saint Faustina

By holding on to my anger, I was letting this instance take control of my life. It was sitting on my shoulders, whispering in my ear, "Don't be happy. Don't do what you want. If anything is wrong with you, it's his fault ok?"

I was not myself. Because I had used this anger as an excuse to remain silent, I found myself distancing myself from my new friends. If they did not understand my problems, then they never would understand me.

Eventually I figured out that by holding back from forgiveness that I was living in sin. So yesterday I decided to go to Confession. I spent most of the day listening to Christian music and praying the Rosary under my lab desk. After three years, I was finally going to remove myself from this sin, from all of the hate and falsehood, from everything I hated about myself since I started college. This was a huge deal, but no one knew about it

The Confession itself was not a huge deal. I did not feel an enormous release, nor did I feel any different afterwards. The only thing I felt was a need to pray for the grace to forgive the boy who hurt me, and to pray in Thanksgiving for the men in my life that have shown me that life will get better.

I did not change.

Life did not change.

God does not change.

Trust in an Unwavering Lord

Confession is an act of honesty and courage - an act of entrusting ourselves, beyond sin, to the mercy of a loving and forgiving God.

--Pope John Paul 2

Just because my life was not completely changed by the Confession does not mean that God's mercy and grace were not present in that moment. The Spirit granted me the courage to be vulnerable with Our Lord and admit my fault in the midst of my anger.

I am not saying forgiveness is easy

But it is easier when you know that God will always forgive you.

Confession is an amazing Sacrament because it calls us to go beyond ourselves. It calls us not only to see what we have done to others, but it also helps us to more fully understand God's infinite mercy. He wants to forgive us. He wants us to be at peace with Him forever.

When I am hurt by someone, I never forget. Most of the time, I have to move on by myself. They do not apologize. The rare occurrences when they apologize are some of the most freeing experiences.

I get to say, "It's ok. I understand."

And every single time they look at me like I just handed them a million dollars.

When we go to Confession, it is our opportunity to apologize to God. He gets to tell us that He understands, because He really does understand. He was on Earth, struggling through the same situations....and then He was put to death on a cross. Even then Jesus Christ chose to forgive us and love us.

Fr. Mike Schmit once said that Confession was not us getting a second chance with Christ, but rather Christ asking for a second chance. He gives us the grace to try again, to be better, and to love Him more.

Without the act of Confession, it would be difficult to imagine Christ speaking to us and telling us that He has forgiven us. With Confession however, we can hear the words "you are forgiven" and we can (if you wish), see a human face forgiving us for what we have done wrong or granting us the grace to forgive others.

So free yourself of your sins.

So free others from your anger.

Let all of the pain and anger slip away with Christ's love. Then, and only then can you become who you were meant to be: a saint.

And in the words of Thomas Merton:

“For me to be a saint means to be myself. Therefore the problem of sanctity and salvation is in fact the problem of finding out who I am and of discovering my true self.”

Faith for Triple A Batteries: Do not Cry Alone

I have a type A personality, more like a Triple A battery running on the energizer bunny personality. When it comes to getting work done, I am the first to finish, and I prefer to work on the task on my own. People get out of my way. Group projects are my worst enemy, and I live by this Yak.

From the looks of it, I should hate people. This could not be further from the truth. According to Myers-Briggs, I am an extrovert, but my incessant talking proves that point on its own. I thrive off of people being around me, and I love to be the center of attention.

Put these two things together, and you get a girl who needs to do things well who also needs people to like her in order to function. I have to have my life together, and I need people to know that so that they will accept me.

By looking like I had my life together, I attracted many different types of people. Most of them were wonderful, and I know in my heart that they were great friends.

The number of nights I spent alone in my room made me feel otherwise.

But there were was a unique subset of friends that seemed to help.

My Own Projects

These were only a few people, but they were unique individuals who had some form of issue that I could fix. Sometimes it was just by being the listening ear. Sometimes it was by saying something. Sometimes it was by making a major change in their lives. Regardless of how, I knew that through my friendships with them that I was making a difference.

Every time they reflected on our relationship, these friends would tell me how thankful they were for our friendship. 

"We'll be friends forever."

"I don't think I will ever be able to make it up to you."

"You have put so much effort in to our friendship."

Friendships like these, where I made a change and felt good about myself because of it, became the focus of my entire life. I talked about these people to all of my other friends, and I identified myself through those relationships. Why? I was A) successful B) well liked because of it.

I thought that God gave me these friends 

I thought that because I prayed for someone to always be there that this was what I needed.

I put my faith in them.

Faltering Faith

God does not just hand us our answers in pretty little packages however. He does not just say, "Oh yes that's exactly what you needed! I forgot!" and suddenly throw your exact request to Earth. Instead, He gives you something a little different and calls you to grow in to that environment.

For me, that meant taking away those friends or asking me to end those relationships.

People left.

I was so distraught and angry and hurt and confused. I would stare in to the mirror as I prayed furiously for hours, tears streaming down my face and nose dripping and stomach heaving from my sobs. In those moments I felt somewhat like Saint Therese of Avila when she said:

"If this is the way You treat Your friends, no wonder You have so few!"

God did not want me to focus all of my attention of these parasitic friendships, and He certainly did not want me to grow cynical, sassy, and cruel because of them. Instead, He wanted me to find something real.

He wanted me to find Him.

Finding Faith

I had spoken to each of these people about the importance of God in our lives, and I pretended that my faith was strong. My rosaries were honest, but their intentions were no longer clear. My so called "faith" was built on a string of spiteful, angry words and sobs in to pillows.

God called me to be alone. This summer I moved out of my comfort zone, and I was no longer the best in the room. I did not have my life together.

I could not depend on myself anymore.

I could not depend on anyone around me to make me feel whole.

So I turned to prayer.

Saint Felicity

It was a terrible day when I finally broke down and asked for God to help me. My experiments were failing over and over again. My little brother was in the hospital, and my family was unable to talk to me on the phone. All of the other REU students were in their labs.

I was alone and failing at the thing I knew God made me to be.

It took all of me to not cry in front of people. In an attempt to hide my saddness, I rushed to the Basilica. There are four side chapels behind the main altar, so I went in to one of those. Inside, I found the Reliquary, which is a place that holds numerous relics to the saints.

Saint Felicity was there.

Because she was a martryr, I knew that she had enough faith in God to die for him. She chose to be attacked by wild animals and have her throat slit. She chose to give birth in prison.

"Now I'm the one who is suffering, but in the arena Another will be in me suffering for me because I will be suffering for him."

All for Christ.

I prayed that she would intercede and give me strength.

No longer did I feel so upset. Instead, I decided that I would just work harder in the lab. I may be lonely at this time, but if I do something of value, then I won't be lonely anymore. My PI will be happy, and I will be able to talk about something exciting when I get back to Belmont. God gave me this ability, so I would do His will by working hard.

I put faith in myself again.

Anecdote 

Of course that faith failed. Nothing on this Earth is going to last forever.

My cells died again.

My time at Notre Dame was shortening.

Soon I would be back to where I felt lonely, without the friend that I had used to pretend that I was important, without the story that I thought everyone loved, without the fake faith that I knew broke me in the first place.

I lost faith in myself. I lost faith in science.

God did not lose His faith in me. So He showed me where to go.

After I tried to walk off the anger and hurt I was feeling, I came back to the lab. I had set up a new restriction digest so I could pretend to be doing something right before I took my break, and I had to run the gel to check for the DNA sequences. It had never worked before.

I felt completely lost.

So I did what my heart was begging for me to do.

I told God to give me strength.

The other undergrad in my lab came to our little undergraduate corner. He asked me what had happened to my cells, and he tried to make light of it, especially considering his experiments had not been going well up until this week. I could not join in and pretend that I was ok anymore. 

My triple A battery had run out of juice. 

I could not keep up the facade any longer.

Long story short, I started to cry right there in the back corner of my lab. It was the last thing I wanted to do, and I certainly did not plan on crying to the other undergrad. I hardly knew him, and I did not want to look incompetent in front of someone who seemed to be able to do anything. 

God stripped me of my falsehoods and gave me the courage to speak to someone.

After talking to him, I got my first hug since I came here to Notre Dame. It's odd what a hug can do for a person. What was surprising to me was that he offered to give me a hug. All of those people that I had filled my life with to prove that I was important never offered to give me a hug, nor did they make sure I was ok on their own. When I cried to them, they would force me to talk, but my fellow scientist just sat there until my sobs had subsided and I could speak clearly.

Then the grad student made jokes and laughed with me as he reinstructed me on some lab techniques, just so I could smile a little bit.

I returned to run my gel, and as I waited, I decided to read the Martryrdom of Saints Perpetua and Felicitas , which is the story of the saint that I am named after. I figured it would be a good way to pass the time as the gel ran along. I did not expect it to work, but I expected God to make me smile and feel better. There was no way of proving that my experiment worked, but I knew something had to happen. God could not just leave me alone like this.

"Faith is to believe what you do not see; the reward of this faith is to see what you believe." ~Saint Augustine

My digest worked. 

After five weeks of trying to do it on my own, I finally asked for God to help, and it worked.

Learn Better

This moment was God's reminder to me that life is not based on who thinks we are important, and it does not matter if you are absolutely perfect. He reminded me that I could not do everything on my own, and He reminded me that He would provide me with every need.

No person should cry alone.

No task should feel impossible.

There is nothing on this Earth that will be unfailing. We can try to be perfect, and we can try to make things last forever, but it not happen as we want it to. That does not mean that life is horrible or that we should give up. Instead it means that we should trust the one thing that will never fail.

Love Never Fails.

God Never Fails.

It's ok to have a Triple A Battery personality. It's ok to try to do as much as possible. It's part of who you are, and it makes you special. We need people who work hard and are independent.

But do not cry alone.

You have an amazing Savior who will never leave you alone. He may not physically sit in front of you, but He will find a way to help you feel better, and He will find a way to remind you that things are going to be better. He will tell you that you are special and loved, even if you did not believe it before.

And then sometimes He will send you people and circumstances that show you that Heaven is for real.

I am so thankful that God loves me so much. I will work for the rest of my life to try to show Him that gratefulness and I will strive to build true friendships and be kind to those who are lonely and lost. I will not hide behind a fake perfect smile. I will not need to cry because I will live as God asked me to.

But if I do cry, I will have God there to listen and friends there to care.

Life is beautiful my friends. Believe that.