Monthly Archives: July 2014

Aha! Moment

I finished my internship yesterday, and finished, as Brian said, “with a bang.”  I was able to run an experiment all the way through, from cultivated the bacteria, to purifying the protein, to running an experiment on how the protein was bonding with peptides.  Even more exciting, I was able to get awesome results that Erin, my postdoc mentor, is going to use in her upcoming paper.  The idea that my figures and my methods are going to be included in a scientific publication makes me so proud.  I never imagined that I would be able to achieve that in this internship!

I think my “aha! moment” also came with the end of this experiment.  Throughout much of my internship, I didn’t feel that I fully understand all the elements of what I was studying.  I didn’t, for instance, fully understand all the different controls that I was integrating in to the experiment.  When I saw how excited Erin was about my results, I decided that I needed to sit down and figure out what I was missing.  With her help, I suddenly felt like I got it!  Flipping through my lab notebook, I could see the process from beginning to end, how each part of the experiment went towards building clear results.  I could also see my own progress.  A few weeks ago, my films were cloudy.  When I purified protein, there were multiple bands that I hadn’t eliminated.  My films yesterday were clean, publication quality.  They indicated clearly where protein was binding.  All of my controls were even and were showing up as we expected.

Part of what I wanted to get out of this internship was to get a grasp of the scientific process, of the thought that went into designing an effective experiment and following it all the way through.  I’ve discovered that not only do I understand, but I was applying this knowledge all along to make my experiments better.  When something was going wrong, I would talk to Erin or Brian to figure out how to make it better.  By the end, I wasn’t going to them at all.  For example, when I saw last week that my controls were showing too much signal on the films, I upped the concentration of the gel I ran so the protein couldn’t “spread” as easily.  I also loaded less with a higher concentration of loading dye.  When I did that, my controls came out perfect!

Now that I have my “lab cred” I’m excited about doing research in the future.  Understanding the process scientists go through every day to build successful experiments will help me design studies in education.  In the fall, I want to look into how augmented reality apps can help my English Language Learners.  Maybe I’ll even look into publishing in some education journals in the future!

Curriculum!

Fun fact: the word ‘curriculum’ comes from the Latin for the tracks on which chariots would race.  I sometimes feel when writing curriculum that I’m figuratively going around in circles.  Writing my Kenan curriculum, however, was exciting because I got to work with content that is new.  I feel most successful in integrating and bridging multiple courses in my lessons: if it works as I plan, students will be able to experience different aspects of genetic research in English, Science, and History all in the same day!

The challenge that I’m having at the moment is translating terms that I’m used to using so that other teachers can understand.  I’m constantly finding in education that we lack a common lexicon: what one school calls PLT’s, another calls PLC’s, or Grade Level Learning Teams, or whatever.  I had particular trouble explaining jigsaw reading groups in a concise way that made sense.  “Jigsawing” is one of my favorite teaching techniques so I wanted to make sure it was clear.  I’m not sure how successful I was, but I’m looking forward to getting feedback next week and seeing what other people are doing!

I found Fellows!

A few family members were in town over the weekend including my two-year old cousin, so we decided to go down to the Museum of Natural Sciences to see the animals.  After spending about 2 hours looking at turtles and butterflies (Nathan, the two-year-old, is surprisingly easy to please), I decided to go in search of the lab where Team Mite works.  I must say, your facility is AWESOME.  I love all the open glass so visitors can observe.  It’s too bad y’all weren’t there.  I would have loved to see some mites!

 

 

Language and Genetics

My original plan for integrating my externship experience into my classroom was to link it up with a novel.  When I began looking at the logistics of this, however, I discovered that I simply wouldn’t have enough time in that unit to add anything else.

I took a new approach: finding the places in my curriculum that needed enriching and then brainstorming how I could apply my new knowledge to give my students a new challenge.

A major part of my 11th grade course is helping students understand how language shapes our thinking.  Genetic research, I realized is fraught with controversy, much of which plays out in popular media.  We hear about “frankenfood” and the “experiement” of GMO foods.  The media tells us that scientists researching cloning are “playing God” and “defying nature.”  The reality which I have experienced during my externship is very different, and a lot less shocking than the media would have us believe.

I have decided, therefore, on a series of lessons that we will complete while my students read 1984 and Brave New World (which pose ethical questions about manipulation through language).    I have selected texts reporting on genetic research for my students to analyze and will give them an assignment to find their own texts and speculate what the influence of the text might be.  The timing of these lessons also coincides with the annual international festival at my school, giving us the chance to research and present on genetic research around the world.  Throughout, I can also provide a counterpoint with my own observations during my Kenan experience.

In other news, this week I successfully completed a peptide pulldown for a protein of interest.  The purpose of the pulldown is to isolate the protein with a series of peptides to see if they bond.  The protein I worked with this week is thought to not have any interaction with the peptides, but what I discovered might prove that wrong…

A Messy Bench is a Happy Bench

This is a picture of my bench today while I was simultaneously preparing protein samples for a gel and quantifying the concentration of protein in the solutions.  It is messy.  It is far messier than my desk at school ever is.  When I first arrived at the lab one of the first things that I noticed is that there was stuff everywhere.  Now I understand why.  A messy bench means science is happening.

I ran into a few bumps in the road today: solutions that weren’t working, gels that weren’t “polymerizing” (I’ve been trained to not say “solidifying” since this is inaccurate), and math.  I’m not confident with math and had to find someone to check all of my calculations after I did them, which slowed me down.  I was reminded, as I foundered with “simple” formulas like C1V1=C2V2, that the part of the value of this experience is getting out of my comfort zone.  Some Fellows might have gotten queasy at the thought of white-water rafting.  I get queasy at the prospect of math.  I also get queasy at the sight of a messy desk, but I’m getting used to it.

I’m curious, fellow Fellows: how has this experience pushed you in ways you didn’t expect?

Technology in the Classroom: My Experience

I am incredibly fortunate that my school embraces and assists teachers in integrating technology into the curriculum.  We have a plethora of technology tools, both to share and to use individually.  We are allowed to have students use their phones for instructional purposes.  We have consistent wireless internet throughout the school.  Students are always eager to use technology in the classroom.

The greatest resistance to technology in my school comes, oddly, from parents.  I think that many parents expect school to be like they remember it, and they may perceive anything involving technology as frivolous or fun (which sadly they equate to not serious learning).  Parents may also feel that their students are at a disadvantage if they do not have the technology tools at home that we have at school.   Students also tend to have a lot more “learning curve tolerance” than their parents do, taking the time to struggle and trouble shoot with a new piece of technology until they learn how to use it.

One of my greatest challenges in created a technology-driven classroom is helping parents understand that their children will need to be technology literate in order to succeed in the workforce.  As cliché as it is, the world is changing and it’s hard for the adults of today to imagine the world the younger generations will eventually inhabit.

Teach Me How to Science

I loved the week at NCCAT.  It’s hard to pick a particular highlight.   I loved getting to know the other fellows, I picked up some resources that will be AWESOME in my classroom, and I got to get back to nature a bit with the beautiful trails and fantastic rafting trip.  I think my greatest take-away, however, is a sense of renewed excitement for teaching.  As much as I am loving my summer externship, I miss my students and being a teacher.  I can’t wait to get back into my classroom.  But, in the mean time, I’ve been having a great time learning how to science (as an English teacher, I can verb words as I please).

I spent most of my first week in the lab following behind postdocs and undergrads lost-puppy style, getting turned around (all 500 liter tanks of Co2 start to look the same after a while), and just generally looking confused and pathetic.  This week I decided to just jump in and give it a try myself.  As with most things in life, confidence, an adventurous attitude, and a little self-deprecating humor went a long way.

I’ve enjoyed a bit of beginners luck.  Over the course of the week I ran protein purifications for 4 different proteins, all of which have been successful.  Purifying protein is like making really finicky, annoying desserts like soufflés or macrons.   It takes 6-8 hours, and the smallest errors in measurement, temperature, and timing can equal disaster (I guess with soufflés or macrons you just don’t get dessert…with purifying protein you’ve lost a week’s worth of work and run through some expensive materials in the process).

The proteins that Brian Strahl and his team are studying are located in the cell nucleus, bound to strands of DNA and other proteins.  Getting just the proteins by themselves so they can be studied in interaction with other proteins and enzymes isn’t easy.  After cultivating the bacteria (while forcing them to retain the desired peptides), you then have to destroy the cells.  Destroying the cells is my favorite part (mwah-ha-ha-ha).   You can either use a sonicator, which blasts through the cells with high-pitched sound frequencies, or you can use the “French Press.”  The French Press isn’t the lab coffee maker; it’s a high-powered hydraulic pump that puts the cells under extreme pressure, causing them to implode and break apart.

After breaking apart the cells, you have to run a series of reactions to isolate the protein.  After each of these reactions, the solutions have to spend time in the centrifuge to separate the good stuff from the waste.  It seems like centrifuge time makes up the majority of those 6-8 hours.  Fortunately there is plenty to do while you’re waiting.  There are gels to prep and buffers to mix.  The purpose of the gel is simply to verify that the protein you want is in the final “elution.”  Science can be rough: after the days of preparation and those 6-8 hours of protocol, sometimes the protein is in the elution, and sometimes it isn’t.  And, often, a lack of protein in the elution isn’t the result of a “mistake” on the researcher’s part.  That particular protein just needs a tweak in the protocol (and good luck figuring out what that is).

Considering I only kind of know what I’m doing, successfully eluting 4 proteins in a week makes me feel really lucky.  I may plan a trip to Vegas.   Here is one of my gels from the week:

gel 7.2.14

The blue bands showing up on the gel indicate protein present in the solution.  I loaded different steps from the protocol in each lane, starting with pre-induction, soluble, insoluble, and elution (the very first lane contains a ‘ladder’ which helps you estimate the presence of a particular protein…more on that soon).  In the first three lanes, there are multiple proteins present because the protein of interest hasn’t been purified in those steps.  In the last lane, however, there is just one band showing up…the TAF14 protein I was trying to isolate!  I can be confident that that is the TAF14 protein and not something else because it falls on the correct location on the gel.  The gel is designed to allow molecules to pass through with an electric current.  The smaller the molecule, the farther it travels.  The ladder places colored lines at various points along the gel, indicating the approximate size of the molecules at that location.  By estimating the size of a molecule in  kilodaltons, you know where it should appear on the gel.

All this, believe it or not,  is just the first step in the process of studying how these proteins interact.  To extend my dessert metaphor, I haven’t actually made the soufflé yet, I’ve just collected all the ingredients.  Next week I’ll be doing peptide pulldown protocols where I’ll get to see whether or not the proteins I isolated bond as we expect them to…