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 🙂

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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.

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.

Setbacks in the Lab

It’s been about a month now. I have had a project since the first day of the quarter, but it seems that the project which I once thought was mine no longer is. I came back from class today to find an envelope sitting at my lab desk waiting to be opened. They were my primers. Three sets of them — sense and antisense.

Though it may not seem like it, I am really disappointed in myself for the results that I have been getting. I know that it shouldn’t fall on my shoulders because I can’t control if two proteins are to interact or not. I followed protocol and that should be what matters. However, tonight, the night before my biochemistry midterm, all I could feel was frustration over my research. I started my new project today. I ended my first one today too.

This is the first time I have felt so invested in something and to see it not work? Heartbreaking.

I know this is only part of research, and that I have learned so much from this month. But still, part of me feels as if I have let my PI down and my lab down.

Your thoughts?

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