First year Grad student…

It’s been a few months since I last wrote. There isn’t much that has happened, to be quite honest. I started graduate school and am nearing the end of my first rotation. I have two more before I choose my thesis lab and am officially admitted into the program I am in. Then, it will be preparing for qualification exams, teaching, and applying for grants, fellowships, conferences, teaching certificates, etc.

What has been hardest for me hasn’t been classes or finding time to do research. It is challenging to be in two graduate courses, attending seminars and journal clubs weekly, and fitting in a full schedule of research but it has been manageable. What is the hardest is approaching somebody I respect and would be honored to be mentored by and telling them that hey, I want to join your lab and while I know you have three other rotation students coming in the next two quarters, don’t forget me alright? I am not one to speak up for myself and make it known what I want. The last time I really did that was high school and that ended up in a really bad situation (let’s just say I ended up scared of returning to my parent’s place). I don’t like to advocate for myself out of fear and the profession I have chosen to pursue is one that requires one to not be silent and to put oneself out there. Conflict much?

Regardless, rotations have been stressful. Finding your own rotation for winter quarter while making sure you don’t step on your classmate’s toes but also making sure you get what you want is a tricky thing to balance.

I wish I had something more profound or better to say but currently, with very little time left in what I consider the most crucial rotation I can have, nothing really makes sense anymore. I am terrified with the prospect of not being able to join any lab, as I am an incredible liability to anybody who takes me on. More than that, I am not a very strong scientist, one that cannot perform experiments properly and cannot analyze data or read the literature. Why am I in this graduate program then? That is a very good question. I am not sure and I wonder if I will ever find out.

Advertisements

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!

“It looks beautiful”

The first thought that came to my mind when I woke the computer from its sleep state was just one thought. It looks beautiful

I never understood why some people are attracted to research, especially when dealing with molecules such as proteins and DNA that cannot be visualized by the naked eye. It looks like a bunch of liquid, really, as you are going through the various steps of purification. Not to mention, in order to get to this ‘liquid’ phase, you need to go through growing bacteria and harvesting them and getting them — the bacteria, that is — to over express your protein.

And if it doesn’t work, you need to start from step one.

There is a lot of modification that happens in lab. Tweak the concentration of compound A. Add a little more of compound B. Let it incubate longer. Did you wake up your bacteria from the -4C freezer?

Not to mention, you never really know what the proteins are doing in this ‘liquid’ as you are working with it.

But despite all these challenges and the set backs that I have faced in lab, I am still amazed at the way various biochemistry techniques, such as SEC (size exclusion chromatography) can yield such clear, definitive results. If the protein is there, it will elute at the fraction corresponding roughly to its molecular weight. If it isn’t there, or if the protein decided it wants to aggregate and clump together, then the chromatogram will show just that.

There is such a satisfaction with seeing a pure peak, a clear, indicative peak that gives insight into what the protein in this ‘liquid’ might just be doing.

Its trivial, I know. I never understood it, from the outside looking in, reading journal publications on how researchers have this moment of “ah-hah”, how they see beauty in results. Now I get it. I have seen it from the other side. It truly is beautiful when you see the results you hope for, knowing that something you have done is right.

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.

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 🙂

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.

Running an Agarose Gel

All by myself. It seems trivial but in all honesty, to be able to set up the entire experiment, from preparing the samples for PCR to making a 2% agarose gel (even though I forgot the ethidium bromide and had to be reminded!) to preparing the samples, loading the gel, running then finally visualizing the results is extremely satisfying.

Just a couple weeks ago, the postdoc that I am working with had to guide me through each step of the process. Just now, once the PCR was done, she told me to stop it and just let me go. She didn’t even need to check in on me or ask me to verify the steps. All she asked was “Do you remember the ratios?” and then I was on my own. I even had to make more buffer to run the gel in but instead of asking her if it is okay to do it (like I would a couple weeks ago), I went ahead, looked at my lab notebook, and made it myself.

Trivial. I know. But still, satisfying. I love seeing the sample with the loading dye settle into the well. I love seeing colonies grow on LB agar with some antibiotic. I love visualizing the gel under the UV light. All of this. I love it. I can’t be more thankful.

Quick Update 10.30.12

It has been a while since I have posted. Since I last posted a week ago, nothing much has changed. To be honest, this week felt like it went by extremely slowly. I had an exam last week along with a paper due and four or five quizzes (too many to keep track of). Aside from that all, research has just been getting more and more interesting; each day I learn something new and each day I see the results of what I am working on. This is truly a rewarding experience.

For example, just yesterday, I inserted a TEV plasmid into E. coli competent cells and after growing overnight in an incubator, there were colonies on my agar plate. As weird as it sounds, the colonies are really pretty. I don’t know what it is about the small things of this research — growing colonies, seeing bands on the gel, extracting plasmids — but I am absolutely in love with what I am doing. Sometimes, I wish I could just skip classes and run tests all the time. Sure, there were a few hiccups here and there during the first couple of weeks where the bacteria didn’t grow properly or the plasmids weren’t extract or inserted into the cells, but these are minor compared to the end goal. To know that I have been matched with this lab and to be able to truly see the words transform into the laboratory is more than I could ask for.

But for now, this is all I have to say. I am just going with the flow and taking everything one step at a time. Nothing in life can’t be overcome; I just have to keep a positive mentality and just keep pushing forth.