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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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 šŸ™‚

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

Research: Failures and not Measuring Up to Fellow Lab Members

For the first time in a long time, I feel like something is working out, that there is a small flicker in the light at the end of the tunnel. As with many people, we all have our own struggles and find ways to combat them. One of the struggles I have is feeling like I am making the right choices with my future and that I belong where I am at in my schooling and with research and just in general.

These past few days, as I have been spending more time in my research lab as well as reading up on various news going on around campus, I kept coming across a similar theme: these people that I am surrounded by, especially fellow undergraduate students, are so much better than me and are so much more capable than I am. This thought had been running through my head over and over — on replay — and kept me down. It didn’t help that my bacteria didn’t grow the other day or that I forgot the procedure to make an agarose gel or that the project that I am helping my mentor work on wasn’t going as planned.

Regardless, despite all these negatives, I felt like I saw a small flickering light at the end of the tunnel for me. I came to realize (even if I don’t believe it yet) that it is okay for me to not know what is going on with the research, that it is okay for me to not have all these accomplishments and accolades that my peers have because I just got involved a couple months ago. I am new to the world of research. I need to start thinking like a scientist soon. I know there isn’t ever an excuse for failing or for not being good enough or not measuring up to other people you are surrounded by but these are just my jumble of thoughts.

This isn’t my best writing by far, but I needed to really just leave it all out there and see what others have to say on this topic.

Lastly, I want to leave you all with this thought:

Isn’t it strange, however, that we are told to look for clarity in our experiences and various aspects of our lives, that we must seek understanding and clarification yet in the research that I am doing, we start with clear LB broth and overnight, it becomes clouded with unknown matter? And instead of starting from a cloudy, occluded mixture and go towards a clear solution, we start with clarity, proceed into the uncertain, and emerge, after many flickering lights, at the end of the tunnel, victorious in our search for whatever it may happen to be.

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. BeingĀ coopedĀ 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 orĀ re-suspendĀ 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.

A Level of Comfort

With experience, in any field of work or study, comes comfort. I have been a part of this labe for just over 4 weeks now. When I started, I got to pipet samples over and over again into eppendorf tubes. I followed protocols with the postdoc I am shadowing for the quarter watching me like a hawk, ensuring I did everything properly. At the beginning, she even did all the calculations and conversions for me.

Now, though I still follow protocols (since if I didn’t I might be in some big trouble!), I have a lot more freedom. I am left to complete experiments that I start. My postdoc doesn’t need to be around in order for me to complete something. For example, like yesterday. I came by between class and work to load my samples into an agarose gel to run. After the gel ran for 20 minutes or so, I came back to lab from work in order to visualize it and check to see if we got a positive result the second time around. This entire time, from when I loaded the gels to after I finished visualizing them, my postdoc was not in the lab. She was doing her own things and I was left to just complete the experiment. I have to admit, at the beginning, I was a bit hesitant. I felt like fish out of water, but after a split second of this feeling, I didn’t let it overcome me. I started to just go about the experiment like I would have if she were here.

And today, just before she left for her lunch break, she checked in with me to make sure that I was comfortable with the protocol I needed to follow in order to extract the plasmids from the cells. I told her I was okay, that I will be able to do it on my own. And indeed I am okay. Because I got sample at the end of following the protocol.

The samples will be sent out for sequencing Monday. The My bacteria grew nicely and now have found a new home in 4 degreeĀ Celsius.

“Lab Rat”

This thought occurred to me as I left lab for class today. What is a lab rat?

My first experience in a lab, I didn’t know what to expect. I sort of jumped into this after looking for over two years for a lab where I could perform meaningful research and take something away from the experience. Yet coming across this experience I cannot be more grateful.

Today, however, for a second, I felt like I was doing scut work. I felt frustrated that just yesterday, I set up a PCR experiment with 6 reactions. Today, I did the same thing again, except with 14 reactions. It felt pointless. But then I snapped out of it. I began to think of how this was actually, in part, my idea to re-run the PCR since we got negative results yesterday. I began to see how I was actually taking on this myself, even though I am, in actuality, doing a very small part of the larger experiment, my role is still important. If there is no DNA to work with, then the protein-DNA interactions cannot be studied and the rest of the work is futile.

It isn’t for nothing. I really love what I am doing, even if it entails making agarose gels each day and pippetting tiny increments of sample into eppendorf tubes. Results will slowly fall into place.

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.

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 moreĀ finesseĀ and eloquence. Thanks for reading!]