Staab Lab Rap

The past several weeks of summer research have been an incredible experience for me with the Bio. Department of McDaniel.  I feel like my words are not adequate to express my thanks and gratitude for having been welcomed into this phenomenal group.  So, in lieu of my babbling, I’m going to leave you all with a rap that I wrote for Dr. Staab in honor of one of the key inspirational figures in her life: Jay – Z.  This rap, entitled “Lab Girls,” is a parody of Jay-Z’s song “Roc Boys (And the Winner Is…).”  If you would like, look up the lyrics on your own – I’m not going to post them here.  [Note: any drink mentioned below is referring to sparkling cider!]  I hope that you get as much of a kick out of this as I did!

 

Lab Girls (And the Winner is…)

First of all I wanna thank Dr. Staab

She’s the teacher, the most important job.

Thanks to science, and to all the noble fish

McDaniel College for holding all the cash

The Bio Department who taught us life in the lab

The first pub worker with whom we had a clash

And the awesome girls in the lab today.

 

Oh what a feeling I’m feeling life

Thanks for the people who gave us aim

For the research projects that are getting us in the game.

Faulty data will stop our buffoonery.

Oh, and thanks for rapping all the fishes’ eulogies

Thanks to all those who became our friends

For sure, it’s paying off dividends

Yeah, thanks to all the digressors

[-- SQUIRREL!! --]

But most importantly, thanks to you: our professor.

 

The Lab Girls in the building tonight

Oh what a feeling, I’m feeling life

You don’t even gotta bring your data out

We the lab girls of the year, drinks is on the house

Look at how we’re geeking, we gettin’ this down.

You don’t even gotta bring your data out

We the lab girls of the year, drinks is on the house.

 

Put yo’ hands up baby, we just hit a score

Pick any fish in the sea, pick a shore

Take what the scientists figured, then figure more

Cause the primary lit. ain’t yet gotten to the core.

Pick a time, let’s pick apart some data sets

Pick a weekend for placing your bets

’Cause we’ve got some staining coming up

We don’t know what these slides are gonna show

So grab a microscope, let’s check the results

Scope it out and take some pics

They’re beautiful baby, these gems are sick.

Get a label and a box,

Posters and powerpoints to make all day

And then papers to write… oh yay

Don’t forget those lab notebooks – gotta record the process, see

’Cause we’re on our way to SICB, dig me?

 

The Lab Girls in the building tonight

Oh what a feeling, I’m feeling life

You don’t even gotta bring your data out

We the lab girls of the year, drinks is on the house

Look at how we’re geeking, we’re gettin’ this down.

You don’t even gotta bring your data out

We the lab girls of the year, drinks is on the house.

 

HBQ, Verhoff-Van Gieson’s

We got the methods and we got the reasons

Chemical analysis and histological stains

Periodic acid-Schiff and Dane’s.

Now this kinda talk is reserved only for bosses

So double-check your stats, we ain’t taking no losses.

Slide boxes, graphs, and endless reading

Let’s have a toast because we are succeeding.

So first things first,

Get out those beakers,

On three, cheers, and shout “Eureka!”

 

The Lab Girls in the building tonight

Oh what a feeling, I’m feeling life

You don’t even gotta bring your data out

We the lab girls of the year, drinks is on the house

Look at how we’re geeking, we’re gettin’ this down.

You don’t even gotta bring your data out

We the lab girls of the year, drinks is on the house.

 

Sweet, now, let’s ride it out

We’ll be back in the fall without a doubt.

This is superhero music right here, baby

American Gangsta, Jay-Z, the Real Slim Shady

Taking flight

Here we go

Reaching new heights

Ow ow, baby!

 

No Fish Were Harmed in the Making of This…Oh. Wait.

The summer has gone by so fast! I guess that time does fly when you’re having fun.

Well. Mostly fun. Some things can get frustrating.

My project this summer (to be continued…fall semester) has involved the study of gill rakers. Specifically, the study of gill rakers across trophic niches.

Gill rakers = bony or cartilaginous spine-like things that are attached to the branchial arches of the fish (branchial arches are the structures that hold the gills!)

http://www.fao.org/docrep/005/ac736e/AC736E117.gif

Very simplistically, they function like a colander > food particles get trapped and water just flows through.

(Red = food, Blue = water)

The gill rakers also have other cool qualities, like taste buds and mucous cells. But not much is known about their general location on the raker, or what exactly the raker is composed of.

So, since these are feeding structures, my definition of trophic niche = the delicious habit of EATING!

Fish are freaks. This has become the motto of our lab.

It truly is amazing how weird and unique fish are. Seriously. Pretty freaky. I can’t wait to get my own fish for fall semester.

Anyway, to collect data I’ve been doing microdissections and histological (tissue) staining. My results are pretty preliminary right now, but I’ve got the procedure down.

(Some) Things I Have Learned:

–       Microdissections are a good way to raise your blood pressure – good music is a MUST (thank you iTunes Radio – Top 50 Country)

–       Histological staining is like Easter egg staining ramped up 589840%

–       Pandora is a life saver

–       Creative uses for lab equipment

–       Wednesday lunches with all the biology research groups rock

–       While nerve-wracking, the symposium was a very positive and necessary experience

–       ALL THE SCIENCE

–       The Smithsonian is super, duper awesome

–       A sense of humor is crucial (thank you to my teammates and Dr. Staab)

–       Speaking of Dr. Staab…

Favorite Dr. Staabisms (Or, Things that Dr. Staab Said that I Found Hilarious)

–       These cups are from the civil war

–       You have to look for the sticky-outy parts

–       Just add a goodly amount

–       They’re saying random things, does that mean garden burger?

–       Anything about fonts

–       Jazziest

–       SQUIRREL!

–       Is that gonapodium or are you happy to see me? Wait, I haven’t taken the harassment training yet, does that count?

–       I’m the boss, so listen to me (not meanly, but as a compliment. Somehow)

In Conclusion:

Overall, I am so, so incredibly thankful for this summer. Not only did I learn A LOT of new things about science and the research process, but I got a chance to interact with the professors of my major on levels that transcend the classroom experience in all the good ways. I made new friends and had many laughs.

Beyond that, my passion for my chosen path (thus far) has been rekindled. Within the last year, I was questioning my decision to be a biology major, to pursue a career in the sciences.

This summer made me see past that.

Bringing in some poetry (hang in there), I think these lines perfectly describe what I feel, here at the end of my seven weeks:

“An Horatian Notion” - Thomas Lux

You make the thing because you love the thing
and you love the thing because someone else loved it
enough to make you love it.
And with that your heart on a beam burns
through the ionosphere.
And with that you go to work. 

Undergrad research – more fun for the professor?

Ever since I was a young undergraduate researcher at a small liberal arts college (SLAC), I knew that I wanted to work at a similar institution. Along the way, I have collaborated with some of the top scientists in my field, at large research-focused universities where a single researcher can get lost in a slew of graduate students and post-docs. Now that I’ve finished my first year teaching at McDaniel and I’m mentoring several undergraduate researchers, I know that I made the right choice.

Some of you might wonder “What’s so great about undergrad research?” Many PI’s (principal investigators; heads of research labs) prefer to have an army of researchers that are already trained to do the work on that lab’s specific project. Here are just some of the advantages of working with undergrads at McDaniel College.

Undergrad Enthusiasm

I am so impressed with the vigor with which my students dive into their projects. My style of mentoring is in line with the old adage “Give someone a fish, they eat for a day; teach someone to fish, they will eat for a lifetime.” I try to give my students the tools that they need to ask and answer their own questions. First I introduce them to a set of questions in line with my research program for which I think the student can yield some answers. I provide each student with some peer-reviewed literature to help them understand where their question “fits” into the broader picture and show them the techniques available to them in the Staab Lab.

Staab Lab June18, 2014

Katelyn McCabe processing larval fish specimens; Paola Villegas examining slides that she stained yesterday; Rachel Statler optimizing high speed videos; Sophia Fricke and Nick Azat preparing solutions for a histological stain.

Once they have these resources, the sky is the limit! The research this summer has truly been student driven, while I am in the background providing support (materials, advice on methods, training in scientific communication, etc.). Indeed, many of the techniques that are occurring in the lab this summer were brought to me by curious students, rather than my forcing methods on them. More importantly, the students are thinking deeply about their projects, asking spin-off questions, and chasing after those answers. It is thrilling to mentor them through this process.

Resourcefulness and sense of community at a SLAC

When an experiment requires expensive equipment or materials, we question the purchase more carefully than someone at a Research 1 university. In fact, many techniques can be modified so that we can bypass expensive purchases This resourcefulness helps us gain a deeper understanding of the protocols and the functionality of the equipment.

For example, in the Staab lab, we process tissue for histological techniques. Tissue processors are machines that automatically transfer a piece of tissue from one solution to the next, without you having to think much about the process. These machines cost about $50,000. But we can manually transfer the tissue into each solution, and if we understand why we are using each solution, we can better monitor how the temperature, timing, and chemistry of the solution are affecting the tissue.

Not only that, but there is a sense of collegiality and sharing among the research labs.

Here is another more simple example of resourcefulness (and a request!): specimen jars can cost hundreds of dollars from scientific supply stores, but why not save those empty pickle/pasta sauce/olive jars for our pickled fishes? It’s true what they say about one person’s trash…

Sample in a jar

Honing my own scientific skills

Let’s be honest, some of that undergrad enthusiasm leads to big dreams of projects that could fill three Ph.D dissertations. It’s my job to reel in the students and help them realize how to completely answer one question before moving on to the next one. It is tempting for all of us to jump to the next shiny project (SQUIRREL!) but it is important to complete each part of the puzzle before building upon it.

The human element

My reasons for getting into science are likely much different than those at a large research university and as such, my responsibilities differ here at McDaniel. Rather than focusing on grant proposals and a high output of data, I am more concerned that my students obtain a rich learning experience that will prepare them for a lifetime of answering questions. Little might they know, they are providing me with a similarly rich learning experience.

Dicty and the DNA Drama

This summer, I don’t even miss my shorts and flip-flops.  I prefer the lab coat, actually.

Each phase of the fruiting body formation is shown.

Dicty Fruiting Body Development

I have willingly traded summer essentials for lab gear and the opportunity to work with Dr. Parrish in her Dicty lab.  We have spent the past three and a half weeks working on Dictyostelium discoideum.  This social amoeba is fascinating, as it is unicellular when properly fed, but cells will aggregate and differentiate to form a multicellular fruiting body which will release spores once conditions improve.  For my particular project, I am focused on a gene similar to the L534 gene in Mimivirus.  This L534 gene is responsible for coding a mRNA decapping enzyme.  My interest is in characterizing this similar gene in Dicty by observing the phenotype of Dicty without this gene.

Cell cultures are displayed on a device used for counting the cell concentration.

AX3** cell culture on left and L534 KO cell culture on right, on a haemocytometer for cell counting. (Click for a larger image.)

Previous research students have created the Dicty L534* knockout, and my task is to study the impact of the L534 gene’s absence to develop a better understanding of the gene’s function and importance in Dicty’s development and survival.  There are three stages of my research which will provide details that we are seeking about the L534 gene in Dicty:

  1. Confirming the Knockout
  2. Observing Growth Rate
  3. Observing Cell Differentiation

The Dicty cultures have finally become healthy enough for completing these phases of the L534 knockout characterization, however, we have reached a snag in our master plan.  To confirm the success of the knockout, we must extract genomic DNA from the Dicty and amplify it though PCR as well as visualize it through gel electrophoresis.  We have completed the extraction and PCR, and we have run the gel, but much to our dismay, the DNA seem to have been degraded.  Confirming the knockout is imperative to the continuation of the L534 characterization, as without the proper knockout of L534, we could not study the effects of the gene.  And so, we have reached a determinant point.  We will be repeating the genomic DNA extraction, PCR, and gel, and the outcome will either “make it or break it.” Stay tuned for the resolution to our obstacle…


*For convenience, we call the gene of interest in Dicty “L534,” though this is the name of the similar gene in Mimivirus rather than the actual name of the gene in Dicty. **The AX3 Dicty cells will serve as the wild type as a means of comparison.  The AX3 cell culture is a strain of Dicty that can be grown axenically, meaning that it is grown on a nutritional substitute (HL5 medium) rather than the bacteria on which it normally feeds.