Save those samples!

I let out the biggest sigh of relief when I saw those three letters in that 1.5 mL eppendorf tube sitting in my box in the -20C freezer.

It has been a couple months since last posting due to the fact that a lot has been going on in my life personally and academically. I have just gotten a chance to sit down, today, with my PI to discuss the project that I am currently working on and all the results that I have gotten.

A time crunch is an understatement for the situation that my project is in. I have been working on this since February, and since the middle of March, my project has been going in circles. Finally, after somewhat conclusive NMR data and yet again unexpected SEC-MALS data, we (my PI and I) have come to the conclusion that quite possibly, something as minor as a His-tag is affecting my entire protein sample.

It would have helped to realize this sooner, but despite all the failures that I have seen in the past couple of months, it is good to know that all my experiments and tests have not been in vain. Though I am going back to step one by transforming my plasmid with my target sequence into E. coli for overexpression, at least I know that what I am about to work on will give me a shot at producing some results at the very least.

My first year at Northwestern is coming to an end and my time in lab has been nothing short of amazing. I have pushed myself to so many limits and cannot have asked for a better lab to join. The people I work with are so incredibly talented and though it often times makes me realize how little I have accomplished in my life and how much of a failure I seem compared against my fellow labmates, I use that to drive me to do what I need to do.

I am motivated and determined to be able to push my project forward. It really is satisfying to see results coming out, to be able to interpret them on your own, and then discuss with your PI in a two-way conversation regarding what the next steps are.

This year has been such a whirlwind but I can say that I am so happy and grateful for the grant that I have been given to allow me to continue my research here during the summer months.

For now, this is it. Bacteria cells await my care. Just know, saving samples is crucial when doing research! Save those samples!

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Back at the bench: in the dugout and in the lab

There is a strange about standing over the pH meter, watching the numbers rise — click, click, they sound. Or so I imagine. One drop too much of NaOH and there goes the beautiful click, click; it is a swoosh, an adrenaline rush.

Time to add HCl. Bring those numbers back down. But one too many drops — even half a drop — and there goes the delicate balance between hydrogen ions and hydroxide ions

There is precision to the work that I do for my independent study course. I am to spend whatever time I wish to in lab, to do my project at my own leisure. Sure, there are ‘deadlines’ I need to meet — have you purified yet? Did you run SEC? How about that protein gel? Do you have enough pellets in the -80C freezer ready to go on any given notice?

Yes. Yes. Yes. I think. No. I actually don’t have my act together. Or I didn’t. Because for the past 10 days or so, since the quarter started, I told myself that I need to focus on me, that I need to start reaching back to the old me — the one that loved to run and workout to stay sane, the girl that found joy in burying herself in her studies.

But that hasn’t worked. Back at the bench since my last class ended, following a day since my 7AM 4-hour emergency room shift, I find myself sitting at my lab desk, staying late into the night, doing one too many tasks. Run the agarose gel to see just exactly why your mutagenesis isn’t working. Incubate the EDTA with your resin in the cold room for 10 minutes before you elute. Collect your fractions from the SEC run and store them so you can run a gel on them later.

There is a list of tasks running through my head. It has been 15 hours since I was last sleeping. I tried to avoid coffee all day but half a cup down and I am going strong.

Fueled not by fear, but by passion. Back at the lab bench, it brings me back to the days when I had a seat on the bench. In the third base dugout, where despite convention of the home team getting the first base dugout, our team was, sun behind us and not in our eyes. Being back at the bench is just like being on the bench, up against the fence, cheering on the team. It is just like grabbing my battered Mizuno glove off the yellow bench, running out as I slip my sunglasses over my eyes, and looking back at the field to gather the sign and position myself, predicting where the ball will go. Because isn’t that what I am doing now? Making predictions and then running an experiment to see if what I think is reality? Because isn’t positioning yourself just slightly on the third base foul line indicating that an inside pitch is being called by the catcher and that the righty at bat will pull it down the line?

At the end of the day, I can tell myself I need this time for this and this time for that. But really, it doesn’t matter what my ”excuses” are, because this is where I feel at home. There is a feeling of serenity and calm that overcomes me as I methodically go through each step. I have my protocol memorized down to how many grams of each chemical I need. Step by step, walking a fine line.

Just like I knew the hitting signals and the fielding cues, I know my protocol. I know that an outside pitch requires me to go with it and poke it just over the first basemen’s head so I can beat the right fielder’s throw to the bag. Just like that. It is a science. Softball and research. Where I am me.

Research Grants

Only having been in involved in biological sciences research since January of this year (when I got my own project, not counting the shadowing I did during fall quarter), the grant process was something that I dove into head first. I knew that the entire process would pose many struggles — composing something that isn’t an english paper? read through scholarly articles to gather background information? understand the entire project? produce preliminary results?

It was all over my head. There were one too many drafts that I ended up going through. At one point, my project changed, and half my grant went out the window. New background information. More sources to sift through. Learning my new samples.

It is an experience that I hope to be able to go through again in the future. I know that I have a long way to go, as I am still very much an amateur in every sense. It has only been a mere three months that I have been working intensively on my own project.

That is what summer is for. Spending time on the shores of Lake Michigan, hoping to understand how two proteins interact. Unsubstantial? Maybe. But I know that it is an honor to be granted this research grant by the university and I can’t wait to dive head first into the coming summer months.

Rhythm

I didn’t think that I would start to enjoy lab when I first signed up for this experience. I did it because I fit the need to step out of my comfort zone and challenge myself at this new school I found myself at in the fall. Yet somehow, over the course of the past few months, I have grown to love the work that I do and love the time that I spend on the fourth floor of Cook Hall.

It has been a busy quarter, filled with an enormous amount of firsts. There have been milestones though. I wrote my first grant. I made my first research presentation and then presented it to my labmates during meeting. Small steps which seem like nothing but mean so much.

What I have come to see is that research is tedious at times; challenging, time consuming, draining, and downright frustrating. But regardless of whatever feelings it may arouse, I know that it is something that has grown on me. Just like you can’t judge a book by its cover, don’t discount all the negatives about what you know of research, because you never know, it could grow on you and add more to your life than you could ever imagine.

Back to the Grind: 2013

There are certain things that I feel as if I will never be able to wrap my head around. Nor will I ever come to fully understand the implications of many of the things that have been happening in my life recently.

Are there reasons why I am so fortunate for being able to come across this opportunity to research in a wonderful lab? What is the purpose of my deciding to push through with a quarter filled with endless hours performing lab research, understanding my project and its implications, as well as trying to keep up with very time consuming, content filled courses?

I guess this isn’t the place or time to be thinking about all of this. I can say though, that after a week back at school in 2013, I am very overwhelmed and wondering what it is I can cut out from my life in order to really, fully grasp everything this quarter has to offer, as well as push myself and do the best that I know I can do.

Overall, I am looking forward to tackling the project that I have been given by my PI. I feel like it is a great starting point for me to really come to understand how to study eukaryotic transcription at the molecular level, something that is truly fascinating and intriguing. Aside from doing basic preparations I have been reading up on the literature written about the proteins I am working on. There is so much unknown out there that it is amazing how I get to be a part of this discovery process. We may think science has offered us all the answers but to this day, there is still so much unknown, so much uncertainty that only through research and discovery will we be albe to come one step, one baby step, closer to understanding how our body works on the molecular level.

Sneakpeak from Within

Next week marks the beginning of my seventh of twelve finals weeks. It is my first time taking final exams here at Northwestern, and as I think about the looming exams and projects due, I can’t help but feel like a freshmen all over again, at UCLA, sitting there being terrified of the one (yes, one) final exam I had during my first fall quarter in college. It was my math 3B exam and I had all week to study for it since the test was on Thursday. I remember sitting in the lecture hall in Humanities (A29 or something?) and staring out in front of me, the exam sitting there waiting to be filled in. By the time I had gotten off the plane and walked around the Apple store at Valley Fair, my exam score had come in. I didn’t fare too badly.

Thinking of this, I am terrified of walking into my first final exam here at Northwestern next Monday at 9 AM. I shouldn’t be worried but yet I am. I have done this so many, many times already. What can be different about these next four exams next week?

Regardless of whatever this fear is, I wanted to share a bit from inside the lab. I snapped some photos using my phone when I had downtime during lab and thought some of these images were really cool. Hope you all enjoy them as much as I enjoyed performing the tests ūüôā

Test tube racks

Test tube rack — eluting DNA

Visualized gel

Imaged protein gel

Making protein gels

Making protein gels

Running protein gels

Running a protein gel

Plating E. Coli on LB agar plates

Sterile technique

Playing with fire

Playing with fire

Plating E. Coli

Plating E. Coli

Resuspending a pellet

Resuspending a cell pellet

A Calm Amidst the Storm

Strange, right? It is something that I have been thinking about lately. What is the one thing that keeps you grounded and focused when the rest of your world is falling apart and spinning to pieces?

For me, that is lab. It is this experience. I went into my undergraduate time thinking that I will never set foot in a wet lab because that is something that I cannot see myself doing ever. Being¬†cooped¬†up inside a research laboratory, sitting in front of an illuminated computer screen late into the night analyzing data, was something that I told myself — promised myself and others around me — that I would never in my life. Thus, I started seeking out clinical experience and dry labs to participate in. I found a clinical lab to volunteer in my first year or so at UCLA but then, when things got rough in my personal life as well as with the transfer process, academics, and my job, I decided I needed a break from the volunteering and to reevaluate all that I want out of my life.

It really came when I received my rejection letter from applying to be a Resident Assistant for my junior year. All my goals and aspirations from before this moment seemed so solidified; I was motivated and ready to tackle it all head-on. But then that one email changed everything for me. Drastic? Not really. From the time I received that email, I have been reevaluating things since. I have decided to venture down a road I promised myself I would never go down: to pursue medicine and go into molecular biology research.

That all said, I am so glad I decided to go down this path. In spite of everything that is happening in my personal life right now, the time I spend in lab is what keeps me calm. It is the place I want to go and am willing to go to after a long night, a long day in class, or just the typical day. Regardless of what it is I am doing for other aspects of my life, I am willing to drop everything and head into lab to make some acrylamide gels or grow bacteria or re-suspend pellets.

Opportunities like this come once in a lifetime, I like to think. Things fell into place in order for me to receive this offer and opportunity to work in the lab more full-time for the remainder of my undergraduate career. Sometimes I feel like the toys which toddlers play with, where there are various shapes and they need to be placed through the corresponding holes. It is as if there are thousands of shapes waiting to fall into place, and the one that has fallen into place is lab.

Even though there may be 999 more shapes that slowly need to fall into place, I am not worried. Why? Because though things may be a bit stormy right now in my life, I have lab, this calm amidst the storm. I am able to focus and clear my mind for just a few hours a day when I put on my hat as a research assistant for the Northwestern University Department of Molecular Biosciences.

Seeing Results: A first successful experiment

I started a little over a week ago at my lab. I haven’t received my own project yet as I am shadowing a post-doc in the lab, learning the techniques that are employed when conducting actual research projects.

To start, I was asked to transvect three different plasmids into E. coli and then extract these plasmids from the bacteria, linearize the samples, and obtain the linearized DNA to save for future use.

My first attempt in transvecting these bacterial cells with the plasmids didn’t go as smoothly as planned; after regrowing the bacterial culture with the transvected cells a second time, the plasmids were successfully extracted from the cells and concentrated so that all I had in test tubes was plasmid DNA. With this circular DNA, I got to linearize them using restriction enzymes and then proceeded to perform PCR to allow the DNA to amplify. After PCR, the products were run on a gel to check and make sure that the samples indeed were linearized properly and that the bands were of the right length.

Then, when all this was done, I expected to start on a new project, to learn a new skill. But I was wrong. Yes, I learned a new skill but I was not given anything new to work on. Instead, the post-doc showed me how to, after imaging the gel, extract the DNA from the gel and proceed to obtain this linearized DNA only. Even though I used a pre-made kit in order to extract my DNA from the gel, it was fascinating to see how all this is done. I never thought that I could do anything with the gel and the DNA bands that are produced. In the past, after imaging, the gel was discarded and that was it. The DNA was never saved. But I have always wondered, how do labs get such large quantities of linearized DNA of a specific vector if the only way that a vector can be amplified is by transvecting bacteria? Well, I have my answer.

I love lab. I love learning, how hands-on the entire process is, and how everything that I have learned in my past classes are actually coming alive and are applicable. I am glad I chose the major I did. I absolutely love it. And I can’t wait to learn more as the year goes on.

[Sorry for the lack of coherency in some parts. It is a pretty stressful week with several quizzes, a midterm, and a midterm paper due for me. Hopefully, I will begin to write more after all this is over and write with more finesse and eloquence. Thanks for reading!]

Starting from simple tasks.

They told me that as an undergraduate, all I would do is wash their used dishes and pipette microliters of substance a thousand times over. They told me that I would not ever do any meaningful research and that professors despised undergraduates.

Whoever told me this, I didn’t want to believe them, but I did. Rumors, they were.

I am glad that I kept an open mind going into my junior year. By doing so, I was able to meet somebody who knew a professor who was looking for an undergraduate to research in his lab and it just so happend the work the lab is doing relates to my interests.

I have been in the lab for a week. I have gone in three times now. Each day I have done something different. I have prepared bacteria to be transvected with a plasmid and grow, I have extracted plasmids from the bacteria that were grown, and I have made broth in which bacteria can grow. Each task, as simple as it may seem, has been a learning experience. I have not had to wash any dishes. I have not had to pipette micro quantities a thousand times over. What I have done is followed protocols. I have followed instructions given to me and been left alone to complete them. The post-doctoral student I am working with this quarter has helped me each step of the way, explaining why things are the way they are and then leaving me to do what i need to to. Nobody watches me like a hawk. And yet I am entrusted with the most basic yet critical tasks for running future experiments.

WIthout the work that I am doing now and the techniques I am learning, I will not be able to perform any future projects. It is critical (at least for the research the lab is doing) that bacteria can grow in large quantities and that plasmids are available in large quantities to work with and manipulate for future studies.

Everything I am doing has meaning. Everything I am learning has value. Nothing is mundane, nothing is useless.

I am building the foundations of what will eventually lead to an independent project and maybe even something more. But for now, I am taking it slowly, taking it one step at a time, and soaking it all in.

Words Come Alive.

Experiences shape the life that you live. I slowly come to think, each day, that this chance — this once in a life time opportunity — really has been a blessing, in a sense. I don’t strictly believe it is a blessing but I do believe that it is fate that I ended up here, that I have made the decisions I have made thus far.

Three weeks ago, when I first came to Northwestern, if you were to ask me what I think I would be doing at the end of the second week of the quarter, I would have told you I would be scrambling to find a lab to join, be swamped with coursework and horribly behind, and lost without friends. But at the end of two weeks, I can say I love this place more than anything, that I want to stay here for as long as I can, and make the most of this opportunity.

Academics aside, I am so lucky to have this chance at research. It just happened that last week, when I attended an informational meeting for a research workshop program I am a part of, as I waited to talk to a facilitator who’s interest lie in genetics (like myself), another facilitator came up to me and struck up a conversation. Research interests came up at one point and it just so happened that the Principle Investigator (PI) she worked for during the summer was looking for an undergraduate student. And it happened that the research this PI is doing is something that is very intriguing and is a field that has a lot of room to grow.

So here I am, two weeks into my last two years of my undergraduate career, spending my time in the research laboratory, playing with Escherichia coli (E. coli) during my free time. It is a post-doctoral student that I get to shadow this quarter, with the opportunity to grow and learn, to get caught up to speed since later on this quarter and for sure starting next quarter, I get to take off on my own project. The topic? I have no idea. I received a couple of papers to read up on what may potentially be the topics of my project but nothing is set in stone. This unknowing breeds my curiosity; it drives me to want to keep working and learning as much as I can, because I can only grow from here.

This post is titled “Words Come Alive”. Why, you may ask? The driving force (and my motivation) for me finding a laboratory to join is that I love to learn but the things I learn, I look to apply. I seek to be pushed to ask questions, to continually learn, and to see how the concepts I learn every 10 weeks translates into actual research. And these first two days, that has happened. Yesterday I got the chance to prepare E. coli with various plasmids which, after treatment with enzymes and other chemicals (which I cannot recall right now), was incubated overnight. When colonies were gather, these were grown in liquid culture for greater quantities.

Today, when I went in to lab after classes ended, the colonies had grown. The plasmids were taken up by the bacteria. All we had to do now was to extract these plasmids. Easy, right?

It is, the concept that is. All you really had to do is open up the bacterial cells and then isolate the plasmid from the rest of the cell contents and the bacterial genome, purify it, and there you go: plasmids. I learned this in class, in my molecular biology class. Yet it doesn’t really make sense on paper (at least for me it didn’t).

But I got to do it today. In about two hours, I created two small vials of plasmids which can be stored for later use. Later use, that is, in experiments, such as when a researcher wants to linearize the plasmids to run them on a gel or insert them into a new genome for further study.

Yes. This is tiring. Yes. This path I choose is exhausting. But yes, this is the most rewarding thing I can think of at this point in my life. I regret no decisions I have made thus far. Things will slowly fall into place, and this dream is worth chasing.