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.

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Proteins

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This is what science is to me. The white powder simply is nothing to most but I know that my protein sample is preserved, that the purification and care I took in processing the cell culture worked. Because that powder is my protein. And that protein is mine.

Cell Biology Videos :)

I think I mentioned before that I have been accepted into graduate school and will be working towards a PhD in biological sciences. However, I don’t know what exact discipline I want to go into but the good thing is I am part of an umbrella program so I get to rotate in three labs and choose!

So to preview I guess what I may be studying — cell biology!

Enjoy 🙂

Hello :)

Hi there readers!

It’s been quite a while since I last posted. All I can say is that life happened, in a good way though. I have finally figured out what I want to be doing with the rest of my life and it’s nice to know I will be staying put here on the shores of Lake Michigan for a few more years!

I applied to the graduate program at my undergraduate institution and was accepted, so I get this wonderful opportunity to study what I love, learn new skills and techniques, be surrounded by the best in the field, all while getting four seasons and starting my own, independent life.

It’s weird but I guess that’s what comes with graduation. That’s not to say you can’t take time off or such but this is what I want to be doing and my gut feeling is telling me to pursue graduate studies in a biological sciences interdisciplinary doctorate program. So I am. I would have never thought when I transferred universities, let alone just a month ago. Sometimes things change quickly, other times slowly. And patience, as I have learned, is the best way to approach all the curveballs life throws our way.

For now, I end with this thought, something that has given me a new way of approaching life. More soon, and I cannot wait to share with you all and document my journey through a doctorate program.

Challenges and obstacles on the path of life may seem initially like things that are standing in your way but in reality, the obstacles, roadblocks, challenges, curve balls are the path of life. You can’t avoid hitting a curveball when it comes your way because if you do, then it will keep coming back. So why not just go for it? You may miss the first time but you will eventually get a hold of it and drive it right over the shortstops head into left field.

Just a thought…

It’s been a while since I updated…

However, I did make quite an interesting observation this morning in lab. Terrific broth cultures, after subjecting them to denaturing conditions with GnHCl, are not pleasant to work with. After spinning down my cultures and getting ready to incubate them for purification, I proceeded to add 20% bleach to the tubes to make it easier to clean. Instead, the solution turned a bright orange upon addition of the bleach and it foams and smells really bad.

I let out a squeal because it was nasty. I can’t shake the smell or feel of it right now. Good thing I was wearing gloves because bleach and bacteria are no good combination ever.

Lesson? Lab safety! You never know what two chemicals can do when placed together.

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.