An untitled post about my advisory meeting and a busy semester

Recently, several different groups of people have been asking for permission to use my photos which always is very flattering. Currently, the Clark homepage is using my picture of the Jonas Clark building. Just below that picture on the front page is a video I made, which is a part of a series asking Clarkies what their favorite things are from area restaurants to classes. The Graduate School at Clark has also asked me for my permission to use my photos, but they haven't picked them out yet. Additionally, I've been asked to share my pictures and videos from our October snow storm to be used as part of a new class at Clark that is chronicling the changing landscape of the campus on a historical timescale.

Preparing for my advisory meeting.

At the end of last week (just over a week now), I had my first thesis committee meeting for my master's project. My committee is comprised of my adviser Dr. Robertson, the genetics professor Dr. Thackeray and my undergraduate adviser Dr. Hibbett. The role of my committee is to make sure my project is on the right track, give me advice, and determine whether my work is worthy of a master's degree. This meeting was the first time I've presented my work outside of my lab, so it was a real test of my knowledge and presentation skills. This is something I will be practicing a lot this semester however, since I may be presenting at least thrice more (more about that below). My advisory meeting, save for a few slip ups, went surprisingly well. However, I do have my work cut out for me and it's pretty daunting.

I have the opportunity to present my work at 51st Annual Northeast Algal Society meeting in April, either in a poster or oral format. Additionally, I may also present my work here on campus alongside a collection of research projects representing the Clark Graduate School. These presentations are of course in addition to my thesis defense, which I hope will happen in May.

From my thesis committee meeting and my potentially busy presentation schedule, I have a long list of things I need to accomplish:

• First I need to fix my quantitative PCR reactions, so I can collect data for my project. More on this topic later...
• Second, after I fix my quantitative PCR reactions, I need to complete a lot of bench work that includes growing discrete lines of diatoms, processing them through experimental assays, extracting their RNA, and preparing the RNA for quantification through QPCR.
• This brings me to collecting all of the data I can to support my thesis through many rounds of quantitative PCR.
• In and around here there are multiple experiments and procedures I need to complete to double check on certain things, like sequence my plasmid DNA used to transform the diatoms and check for the number of construct copies each of my diatom lines received in the genetic transformation.
• I also will need to prepare for each presentation and make sure everything is pulled together.

With so many things going on in my research project, I don't think I'll have much time to do anything else. This is of course without considering the work I need to get done in the class I'm helping out with--Physiological Ecology of Marine Algae. It's very likely I will be leading a group research project with 2-4 undergraduate students. This work will be crammed into about 6 short weeks. While I know this will be a great learning experience for me, I know those weeks are going to be very stressful.

From GRE to RT-PCR

The view of Lasry the other day on my way into lab.

A few weeks ago I took the GRE as part of my quest to continue graduate school in a Ph.D. program. Standardized testing is such a money scam given all of the fees involved from taking the exam to getting your scores and sending them to your schools. Furthermore, I don't think standardized exams are particularly informative, which is funny because Clark was just in the news because they are no longer requiring SAT scores for undergraduate admissions.

But I digress: I'm not here to complain how ridiculous the whole process of taking the GRE is. I'm just super glad the GRE is behind me and I can focus on things that actually matter. Yet ever since, I've been taking it slow with my workload because I needed a bit of a break. Thanksgiving marked the end of that break though, and now it's time to jump right back into things to finish up a productive semester.

I have a very hopeful list of things I'd like to accomplish by the end of the semester in mid December. But because I'll need to be working a lot more hours at the bookstore to help with the end of semester rush, it's going to be a big squeeze.

We're starting to get books for the spring semester at bookstore, & they're piling up.

This  picture is enhanced with the iPhone app Cat Effects.

Meanwhile in the lab, I have heaps to do. I want to finish up my experimental assays, screen and grow out more diatom cultures for future experiments, prepare a presentation and do some writing, and finally start with some RT-PCR experiments.

Now previously I extracted RNA from my frozen cell samples and used the mRNA present from the cell samples to generate cDNA.

RT-PCR, or real time PCR, will allow me to quantify the cDNA that I have made from my RNA. This is because RT-PCR can measure the number of DNA copies at each copy cycle by measuring the fluorescence of a special dye that hybridizes with the DNA. This is pretty snazzy, but it looks like I'm getting myself into a lot of grunt work.

You see, in order to get precise data from RT-PCR, one usually runs three replicates from one DNA sample and compares the output. But it's not like I only have one DNA sample. I have tons.

This is because I have 8 DNA samples at the minimum per experimental assay that I run in the beginning: I have two different cell lines that I test per assay, which get divided between two different test conditions, from which I take cell samples at multiple timepoints.

For the time being, I'm going to start with time zero and my end time of 60 minutes. This will hopefully give us start and end data that will display the overall trend of my experiments.

But because of positional effects, I need to run more than one experimental assay. I'll probably run three sets of samples through RT-PCR, but I hope to have up to 5 samples completed and ready for RT-PCR by the end of next week.

This is from today while I waited for my next sampling time.

Wait, what's that positional effects you just mentioned a second ago? Oh, yeah, positional effect. Because we transformed our diatoms with ballistics, our DNA was randomly inserted into the diatom's genome. By chance, the DNA we're trying to measure in our experiments might be inserted into a region that is either expressed more or less often, which would skew our data. By gathering data from multiple replicates, we'll get more accurate data regarding gene expression. Cool how science works, huh? We think of the neatest little caveats. Well, I mean, my professor does.

But sometimes I do too!

Like last month or so I came up with a solution as to why our cultures weren't growing so well. And then more recently I figured out how to screen my diatoms for our reporter gene more effectively.

So yes, sometimes I come up with cool things too.

The Jonas Clark building. I can't stop taking pictures from this vantage point! Gah! I love it! 11/18/2011

Untitled post about science

Science on a quiet Sunday afternoon:

DUN DUN DUN: DIATOM TRANSFORMATION (video edition)

I TRANSFORMED MY DIATOMS. ALL IS WELL. THIS IS AWESOME.

Well of course that is if we successfully transformed the diatoms. There's a 1-2 week grow period during which we have to wait in order to see transformed clones. I'll keep this blog posted and will post a text post regarding the transformation soon as well.

A quiet day in the lab

Apparently I've trained my bacteria really well...

...look what they did last night!

They're super neat! ^,^