This week has been an absolute whirlwind! We’re on the home stretch, friends.
So this week I’ve been splitting my time in the lab with working on my poster and getting feedback from the other people in the ball lab. Cody and Patrick have been especially helpful in the formation of the poster. Thanks guys!
In the lab, we’ve been working on getting some protein for our reactions – with varying results. This is my mentor’s first time doing this, so the first result was a vial full of dead cells. Ooops! The next batch was quite a bit more successful and there was much fanfare, and we were able to culture the cells with some help from Chi’s lab.
Next we had to lyse the cells to get them to express the proteins, then centrifuge the crap out of them. There was quite a bit of back and forth as to how we wanted to split the cells up, but we ended up splitting them into 13 vials (which required a LOT of fiddling to get the mass within one gram of each other).
After lysing the cells and centrifuging them, we extracted the liquid and got some decent proteins! Katie also set up a boronic acid reaction without any oxygen present which I thought looked neat. There’s nitrogen in the balloon, which keeps the pressure above 1 atmosphere.
I got my first draft of my poster done though, and good lord that was a lot more work than I thought it was going to be! I’m going to be relieved when the poster is printed out and I get to see it in all its glory.
Man, this week really flew by! Just as I’m starting to get the hang of things, this whole experience is about to be over. This week, we did quite a bit of testing of our boronic acid mixtures that we set up last week. We’ve been trying to mix up some stuff that’s going to be good for layering onto our surfaces, but testing has revealed that a large portion of our mixtures haven’t worked out. Here’s where the MALDI machine comes in. MALDI stands for matrix-assisted laser desorption/ionization. It’s basically a gentle way of fragmenting our peptides that would be harder to read by more conventional methods.
This is an example of a MALDI machine. The one in the BRC is quite a bit bigger! We also have a speed MALDI, which essentially just gets it’s results quicker.
First, you have to prep your samples to put onto the MALDI plate. These samples have been mixed with a matrix which helps the samples crystallize onto the plate.
Each one of those bubbles represents a single sample. You can run many experiments using one MALDI plate, which makes them ideal for the kind of testing that we’ve been doing.
Once the samples have been read, we get data that looks like this. You can see the different fragments of whatever was on the plate and their molecular weights displayed at the peaks. We can tell if our compound has modified by how heavy the tallest peaks are.
Hopefully next week we can test out our newly modified surfaces and get some more data!
To say that this week has been a resounding success in the lab would be a biiiiiit misleading. We experimented, and experimented, and experimented some more and just couldn’t see the data we wanted to see. We got some good data from out failures though, and I learned some new techniques in chemistry!
The first thing we did this week was some gel SDS-PAGE. It’s a method of separating charged molecules in mixtures by their molecular masses. It uses sodium dodecyl sulfate to help identify and isolate protein molecules.
The first part of the process is to make a matrix with the gel and some SDS. We did this the previous day so the buffers didn’t accidentally mix. Next we prepared the samples!
You actually have to heat up the protein samples so the proteins unfold. They tend to bunch up into little balls, so heating them up along with the SDS helps them to unfold.
After some heating, we squirt the samples into the gel matrix.
And then we wait and apply electricity. The samples move towards the negative pole based on their molecular weight. We had to wait several hours and…
This sample batch was a resounding failure. Oops! We tried several more times and eventually got it right. After you pull out the gel, you have to stain it with a blue dye called Coomassie. It makes the data much easier to read.
The round robin tours were a ton of fun, and I learned that all pretty much all scientists are horrendously messy people! It made me feel better about my lab.
I spent a lot of time catching up on my chemistry last week, and this week has been less observation and more making things helpful to our lab. My mentor has kept me busy and has been walking me through the math to make 50 Millimolar solutions to use in our reactions. Now I’ll be able to tell my students who complain about doing math during science that the two are one and the same, and give some great examples. Maybe it will inspire some of them to take math more seriously!
I was also given the task to study up on a process called “contact angle”, which is used to measure the angle of water droplets on a surface. We use it in the lab to see if some of our modifications have taken to that surface. Our lab uses a boronic acid modification that should change the angle of a water droplet when put onto whatever surface we’ve modified, so we have been doing quite a bit of experiments that involve the contact angle machine. So far our results haven’t been what we have wanted, but the testing continues.
My mentor Katie helped found a program called “Fun with Science” for younger students that visit Rice University. They get to see some of the more dramatic chemical reactions and changes that chemistry is capable of. She let me come to the show to take some pictures and get a few ideas that might benefit my school, and I got to see some fun chemical reactions as well! Students get really excited about chemistry when they see how fun it can be.
Yesterday while Katie was off in meetings, I made my way to the Library and read up on contact angle and spent quite a lot of time searching the stacks for some good books. I found quite a few and read up on the history and math involved with contact angle as well as how to properly implement the procedures involved. Hopefully all that study will come in handy next week as we dive even deeper into our project! I believe that we are making some good progress, and I’m excited to see what next week brings.
Hello all! Welcome to my blog. Okay, so the first week is just about over and what a doozie of a week it has been! Let me give you a little background about myself before we get started.
I got my Baccalaureate in Youth and Family Ministry from Lubbock Christian University back in 2010, and as you can imagine I did not have to take very many hard science courses for that particular degree. In fact I was able to substitute a science course for something completely different, thinking that I would never have a use for it. Boy, was I wrong!
Years later, I decided to teach elementary school math and science. I had to get my alternative teaching certification and struggled a bit at first with the material, but wound up enjoying myself immensely. It’s a bit strange teaching science when you’ve only experienced a laboratory environment in high school so when the RET applications opened up I jumped on the opportunity!
With all that being said, I want you to imagine a pool. One end is the shallow end, where I had been playing with my bright yellow floaties on. The other end is unfathomably deep and filled with grad students and it’s labeled “The Ball Lab”. I decided to jump into the deep end and figure things out as I went along, and it’s been quite the challenge! I’ve learned more about chemistry in the past week than I ever thought I would learn in my lifetime. Dr. Ball has instructed me to observe, and perhaps replicate some experiments for the first week and we will meet and discuss what to do after I’ve absorbed some lessons.
My mentor Katie has been instrumental to my progress, and has been letting me get a great feel for the process of what they do in the laboratory. Her project is to take a surface, and use existing chemistries to covalently bond a one-molecule thick layer of proteins in a predictable and easily replicated way. It’s all still a bit over my head, but I’ve put myself on something of a crash course in chemistry to get caught up and I’m starting to make sense of it all.
If there’s anything that I can take away from this week is that chemistry is sometimes a slow process, involving a lot of experimentation and trying several different things at the same time to see what works and what doesn’t work. I’m also learning that there’s a ton of dead-ends in science, and that those are very informative in that they help you narrow it all down.
K-12 Educators Disseminating Research from Rice University, Arizona State University, and University of Texas-El Paso