doc w/ pen

a journalist becomes a doctor before your eyes

Month: June, 2011

Microbiology In Action

I voluteered yesterday morning and had a new experience there, which was pretty interesting: the convergence of microbiology and clinical work. A woman came in having been treated the previous week for a urinary tract infection (UTI), but her symptoms had returned. The nurse practitioner I was working with thought based on the symptoms that it sounded more like a yeast infection than a UTI. (I had to look up the word for “yeast” in Spanish – levadura.)

So the nurse practitioner decided to take a vaginal swab and prepare a slide to look at under the clinic’s lab microscope. I had no idea the clinic’s lab even had a microscope … I suppose it’s an obvious thing, but I never thought about it, since I don’t really go in there. The nurse practitioner prepared the slide with two specimen samples, and a drop of saline on one of the samples and a drop of potassium hydroxide on the other. I, of course, asked whether I could go with her to look at the slides in the lab. She’s one of my favorite practitioners at the clinic, and I work with her a lot, so she was quite willing.

We slipped the slide under the microscope, and lo and behold, yeast cells. Of course, I spent lots of time in Biology I and II last year looking at slides under the microscope, but obviously never in the clinical context. So it was really neat to be able to actually diagnose something using the same scientific tool we had used in class. Very rewarding.

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ADCOM Q&A (favorite non-science class)

When I was an undergraduate, I took a little of everything: anthropology, sociology, comparative literature, history, philosophy, film, Spanish, biology. And, of course, my major: journalism. I liked some classes better than others, sure, but I’m of the opinion that you usually get out of a class what you put into it. And I generally put a good deal of effort into my courses. In other words, I got a high-quality, well-rounded education at the University of Illinois.

So if an admissions committee member put the following question to me – What was your favorite non-science class? – I would have a lot to choose from.

But “favorite” implies one. So I would have to go with J380. “J” standing for “journalism.” This was the advanced-level reporting class for journalism majors, usually taken by seniors. I took it as a junior so I could study abroad my senior year. I don’t remember the formal title of the class, but we students usually referred to it as “beat reporting.” Because that’s really what it was. For those of you outside the J-world, beat reporting is covering a particular issue, community, or other specific subject. In this class, we had to choose one such topic in the Champaign-Urbana area and write about it throughout the whole semester. We were to write several smaller stories in the beginning of the semester. Then the class culminated in a three-part series of at least 25 pages, which was equivalent to our senior thesis.

I still remember our first discussion section, when we chose our beats. Professor Bob Reid wrote a list of potential beats on the blackboard and we took turns picking from the list. I immediately knew which one I wanted – international issues – and crossed my fingers that no one would take it. I got my wish. International relations, and how they affected the local community, fascinated me. I really wanted to explore the subject. (I should also note that I minored in International Studies and had taken several related classes at UIUC.)

I will be honest: I did not exactly enjoy this class at first. In fact, a couple weeks in, I panicked (especially about having to write that 25-page series) and wanted to drop the course. I even thought about changing my major, since J380 was a journalism graduation requirement. But my advisor told me to stick it out, and I’m glad I did.

Why? Because I really came into my own in that class, in so many ways. As a reporter and writer, sure. But also as a young adult trying to find her way in the world.

For starters, Professor Reid had this thing about Curious George. (Yes, the little monkey who is always eating bananas and getting into trouble.) He said we should all be more like Curious George – wondering about everything we see and hear, touch and smell. And also seeking out new adventures. That is what makes a good reporter, he told us. I really took that to heart. So I didn’t sit around in my little apartment waiting for stories to come to me (that never works anyway). I went out and looked for them. And I mean really looked.

For example: I knew that one of the big international issues in the community was the increasing supply of crops from South America, and its effect on local crop prices. I figured the best people to talk to about that would be some farmers. I found out from an agricultural professor that a group of them met every Saturday morning for coffee in a little cafe a few miles outside Champaign-Urbana. So I made plans to meet them out there. Which doesn’t sound like a big deal, except that I didn’t have a car. So I rode my bike. More than 10 miles, round trip. On the highway. With semis rushing past me as I pedaled by on the shoulder. Not the safest thing I’ve ever done, but I felt it had to be done. I was curious, and wanted some answers to my questions. I learned that pounding the pavement – literally – is the way you get those answers.

One of Professor Reid’s pet peeves was that students rarely thought about accountability. He wanted us to call our local, state, and national representatives, heck, the PRESIDENT, and find out what they thought about what was going on in Champaign-Urbana regarding what we were writing about. You didn’t get an A on a story unless you did that. He didn’t think you deserved an A unless you had gotten that angle. And I came to agree: our government does need to be held accountable (to an extent) for what is happening in our community. So I would sit in the journalism department’s phone room (which was basically a little closet in the basement of Gregory Hall, with two landline phones – this was in the day before most people had cell phones) and call government offices to get their comments.

This was more of a reporting class, but I also learned a great deal about storytelling from Professor Reid. Because if you don’t tell your story well, there’s a good chance people won’t read it. So I gradually became better at weaving in relevant sights, sounds, and smells, as well as dialogue.

And when the time came around to write my 25-page series – which had me practically paralyzed at the start of the semester – I wrote, wrote, and wrote until I realized I had crafted a work of more than 50 pages. And it was not fluff, either. It was journalism. It was then I realized: I was a journalist.

While I discovered, after several years in the publishing field, that journalism is not where I want to spend the rest of my working days, I took valuable lessons from J380. That’s why I count it as my favorite class: it’s stuck with me. In the end, isn’t that what the best classes do?

Better Things Lie Ahead

As I may have mentioned before, I haven’t lived alone in more than 7 years. And back then, I was in a serious relationship (with my husband). So it didn’t feel like I lived by myself.

Now I really live alone – and I’m finding it to be somthing of an adjustment. It’s not that I mind doing things on my own. When I lived with my husband, we were often doing our separate things, but it was in the same house, and we both knew there was another person around. Or another person you could call just to say “hello,” or “I love you.”

Waking up alone is another odd thing. I’m accustomed to having my morning coffee with another person, not even necessarily talking about much, just another person being there, sitting next to me on the couch. Coming home from the lab to an empty apartment, having dinner by myself … they’re all reminders of what has happened. I don’t feel sad all the time or anything. Sometimes I feel a little lost, though, in these altered circumstances. I think that’s normal, but it’s bewildering nonetheless.

I know how important it is, especially now, to socialize with my friends and family. And I do. I have dinners out, dinners in, coffee, etc. And lots of phone conversations. It’s just those weird times when I’m used to another person being around that get me.

Everyone asks me how I’m doing. I tend to say that given the circumstances, I’m coping well. And that is the honest truth. But that doesn’t mean this isn’t hard, or that little things like seeing couples kissing or holding hands don’t send shockwaves of memories through my mind.

A dear friend of mine recently got married (it was both the bride’s and groom’s second marriage). I helped out with planning the wedding. Which I thought might be really difficult for me, but was actually a lot of fun. A few days later, I was over at their house, and my friend’s new husband pulled me aside. He had gone through a very nasty divorce before meeting my friend, and told me that while he obviously didn’t enjoy that situation, he is much happier in his current relationship than he was in his first marriage. So it worked out for the best. He encouraged me that there are positive things ahead in my future, too, and to focus on that as much as I can.

This is a message I have gotten from several friends who have been divorced: that good things, better things, lie ahead. I’m trying to hold on to that as much as I can. Thank you to everyone who is helping me do that.

The Funny Papers

I have fond memories of lazy Sunday afternoons during my adolescence, post-late-afternoon-pot-roast, sitting on the couch and reading the comics section. (That was back in the day when people actually subscribed to newspapers … but I won’t get in to that.) These days, my exposure to cartoons comes from my mom, who saves medically-related “Close To Home” cartoons from her daily flip-calendar and brings them over when we have dinner together at my apartment. A few days ago, she brought one that really made me laugh. I found it online, and thought I’d share it:

 
John McPherson has some pretty funny ones, let me tell you – and I found quite a few that tie into medicine. I’ll post them periodically, because I believe that we all need to laugh a little more.

My Birthday Wishlist: A Histological Study

Smooth Muscle Isolated Fibers

My 30th birthday is in three months and nine days. And let me tell you, I’m counting down every one of those days. Not because I’m particularly eager to be 30 – though it doesn’t bother me at all that I’m about to hit the three-decade mark – but because I’ve discovered what I want for my birthday. All of the Etsy.com science items I recently posted go on my wish list, of course (although I want the colored pencil chemistry labels, rather than the crayon ones I listed – I don’t own crayons anymore). But today I found something else: microbiology posters.

Neurons: Human Brain
Cognition Synapse

No, I’m not joking. And so to answer the question burning in your mind: Yes, the nerdiness continues. I love it.

Ever since last summer, when I started at the research lab, I have been fascinated with stained slides. One of my tasks last summer was to count cell nuclei (which were stained blue, by the way) for Olga. It was pretty tedious, whish one of the reasons she asked me to do it (she admitted as much), but I didn’t mind. I knew I was contributing something. And honestly, the images were just gorgeous.

Blood Clot Formation:
Showing Trapped Red Blood Cells
(Erythrocytes) in Fibrin

So today, after I posted that image of the pancreatic cells, I got to thinking: I wonder whether there are posters of such images that one can purchase? I assumed it must be so, in this day and age of Internet shopping. I tried a bunch of keywords on Google, and finally came across Allposters.com. It took me a little while to find the site’s microbiology subsection, but when I did, I knew I had hit the jackpot. I ended up e-mailing myself more than 20 fantastic posters of green-, red-, and blue-stained neurons; a blood clot formation; red- and teal-stained muscle cells; a purple-, pink-, and blue-stained neuromuscular synapse; and so much more.

The Neuromuscular Synapse:
The Junction Between a
Nerve Fiber and a Muscle Fiber

My living room decor is set, as is that of my bedroom. But the walls in my office / music studio are glaringly blank. In the taupe-y sense. They are just begging for me to hang framed prints of erythrocyes and collagen protein on them. I figure I’ve got space for five or so prints, frames included. It would be so perfect: to study biology, genetics, and chemistry amid such poignant, beautiful, and educational imagery. And what conversational pieces they would be!

Fact or Artifact?

Prior to last week, my only exposure to “artifacts” was something like this:

This artifact is an ancient Chinese pot, the kind of piece you would see at Chicago’s Field Museum, or in a similar collection.

But last week at the lab, Vasily, my research supervisor Olga’s husband, told me about biological artifacts. Here is a definition from Biology Online:

Artifact. Any visible result of a procedure which is caused by the procedure itself and not by the entity being analyzed. Common examples include histological structures introduced by tissue processing, radiographic images of structures that are not naturally present in living tissue, and products of chemical reactions that occur during analysis.

Vasily told me that the researcher has to be very careful to distinguish between what might seem like fantastically interesting results and an artifact. I was intrigued. So I looked up some articles on PubMed about these so-called artifacts. Here are some of my findings, along with some pretty cool images that illustrate the concept.

One type of article that kept coming up was about radiological artifacts. Basically, the idea is that the quality of a CT scan or MRI can be compromised, leading to “image artifacts” that can result in the improper diagnosis of a disease. For example, according to one paper I read*, there are several categories of radiological artifacts. The artifact type that I understood the best (the others had to do with rather sophisticaed nuclear technology) results from motion. If there is either involuntary (i.e., sneezing, heart beating) or voluntary (i.e., swallowing) movement, there could be distortions or shadowing on the film. Above is an example of a artifacts pictured in the paper.

On a subject that I understand a bit better (and that results in prettier pictures), there are artifacts on the biological side of research as well. Another article I found** was about a very specific aspect of pancreatic epithelial cells. Its authors reported that a type of cell transition that had been observed in their laboratory was likely an artifact. They hypothesized that their cell isolation procedure might have introduced some type of genetic changes in the cells that caused the artifactual result. Below is an image from this paper, representing the artifact that they observed: the coexpression of MSC antigens CD29 and vimentin in a two-day cultured pancreatic digest. (Don’t worry if that’s Greek to you. But I know some of you out there are research folks, so I figured I would mention a few details.)

So what’s the point, other than looking at cool cell stainings (which is fun on it’s own, in my opinion)? The point is that as a scientist, and as a clinician, you have to be cognizant of what is normal. And then when results come back that are abnormal, you take a close look to make sure that there is not an alternate explanation other than true abnormality (or perhaps an amazing discovery, in the case of research). It’s always about questioning things. That’s the nature of science, isn’t it? I think so, at least.

* Popilock, R., Sandrasagaren, K., Harris, L., and Kaser, K.A. (2008). CT artifact recognition for the nuclear technologist. J. Nucl. Med. Technol. 36, 79-81.

**Seeberger, K.L., Eshpeter, A., Rajotte, R.V., and Korbutt, G.S. (2009). Epithelial cells within the human pancreas do not coexpress mesenchymal antigens: epithelial-mesenchymal transition is an artifact of cell culture. Lab. Invest. 89, 110-121.

I amplify DNA. Yes, I really do.

“I trust you.”

That was about the greatest thing my research supervisor, Olga, could have said to me. She was referencing my skills at setting up PCR (polymerase chain reactions). And it’s quite helpful that she trusts me with these reactions, because the work in our lab involves doing quite a bit of PCR.

Not only am I precise and accurate with these reactions, I am also building up my speed. I was setting up 24 tubes of PCR last Thursday, for example. Olga came in to check on me and asked how I was doing. “I’m done,” I told her. “You’re done?” she asked, brows raised in surprise. “Pretty soon you’re going to be a machine!” Another high compliment from a highly intelligent woman with a PhD who can pipette with lightning speed. Compared with my snail’s pace from last summer – when I came in not knowing what a pipette was, and certainly not knowing how to use one – I’ve come a long way.

While those of you familiar with lab protocol likely know what PCR is, most people don’t. I certainly didn’t until last summer, when Olga expertly and succintly explained it to me. It’s quite marvelous, really, how it works. I thought I would take a blog post to explain it, since it’s been such a big part of my lab work lately.

The goal of PCR is to amplify a specific region of DNA. There are three steps in PCR: denaturing, annealing, and elongation. These are fancy, scientific words for breaking apart the entire strand of DNA, using what is called “primers” to bind to the broken-apart DNA, and then employing a special enzyme called taq polymerase to synthesize a copy of the specific DNA region you want. You do this through cycles of heating and cooling to promote these different steps. This yields an exponential amount of the region of DNA you want. Pretty cool, eh?

Here is a visual representation of the process*

The technique was developed in the 1980s, and in the 1990s, its inventors were awarded a Nobel Prize. It’s amazing to me that less than 30 years ago, we did not even have this technology. Science has come such a long way, and I am thrilled to be a part of it.

*This image was downloaded from the online edition of: Molecular Cell Biology. 4th edition. Lodish H, Berk A, Zipursky SL, et al. New York: W. H. Freeman; 2000.
Available on the NCBI bookshelf: Molecular Cell Biology

Musical Mixing: My Personal Anthem

I love music. Always have. One of the things Geoff* taught me was to create music “mixes” on iTunes. Great fun! I especially like creating themed mixes – for example, I made one using songs that are about animals, one about war, one about colors. I am in the process of creating one I call my “Personal Anthem.” It includes songs that I find encouraging, inspiring, and of personal meaning. One song I recently came across is The Roots “The Fire,” which I will definitely work into that mix. I want to share the lyrics from that song. It is about ambition, and not giving up – a poignant message for any student, or anyone at all.

“The Fire,” by The Roots

[Chorus]
There’s something in your heart,
and its in your eyes
It’s the fire, inside you
Let it burn


You don’t say good luck
You say don’t give up
It’s the fire, inside you
Let it burn


Yeah, and if I’m ever at the crossroads
And start feeling mixed signals like morse code
My soul start to grow colder than the North Pole
I try to focus on the hole on where the torch goes
In the tradition of these legendary sports pros
As far as I can see I made it to the threshold
Lord knows I waited for this a lifetime
And I’m an icon when I let my light shine
Shine bright as an example of a champion
Takin the advantage never coppin out or cancelin
Burn like a chariot, learn how to carry it
Maverick, always above and beyond average
Fuel to the flame that I train with and travel with
Something in my eyes say I’m so close
To having a prize
I realize I’m supposed to reach for the sky
Never let somebody try to tell you otherwise


[Chorus – John Legend]
There’s something in your heart,
and its in your eyes
It’s the fire, inside you
Let it burn


You don’t say good luck
You say don’t give up
It’s the fire, inside you
Let it burn


One love, one game, one desire
One flame, one rhyme, fire
Let it burn higher
I never showed signs of fatigue
Or turned tired
cause I’m the definition of tragedy turned triumph
It’s David and Goliath
I made it to the eye of the storm
Feeling tore like they fed me to lions
Before time start to wind down like the Mayans
I show ‘em how I got the grind down like a science
It sounds like a riot on hush
It’s so quiet, the only thing I hear is my heart
I’m inspired by the challenge that I find myself standin eye-to-eye with
To move like a wise warrior and not a coward
You can’t escape
The history you was meant to make
That’s why the highest victory is what I’m meant to take
You came to celebrate
I came to cerebrate
I hate losing I refuse to make the same mistakes


The fire, the fire…


[Chorus – John Legend]
You say don’t give up
It’s the fire, inside you
Let it burn


The fire, inside you (x3)
[End]

I find myself listening to this song over and over, in part because I love the music, in part because I love the lyrics (I’m a big lyrics person, clearly). I don’t know the rest of the album, but you can get this one song for $1.29 on iTunes. That’s less than a 20-ounce bottle of soda. If you’re looking for a positive song with a good beat and you like spoken word, this is it.

*Geoff is my soon-to-be ex-husband, for those of you who haven’t read some of my recent posts.

These Are A Few Of My Favorite (Science-y Artsy) Things

As an artistic person, I love looking at other people’s work. Etsy.com is one of my favorite sites – there are literally thousands of other artists and crafters on there, selling their wares. A couple of days ago, I decided to see whether there were any science nerds creating arts and crafts. And by jove, there are. Here is a collection of hand-picked favorites (in no particular order). I have included a link to each one in case you are inclined to visit the person’s store and purchase something, which I wholeheartedly recommend!

AUG start codon “new beginnings” necklace ($100)

Those of you who know me well know how much I love proteins. And every protein starts with the amino acid sequence “AUG” – the so-called “start codon.” So how could I not love molecularmuse’s necklace?

Liver In A Jar Anatomical Curio ($19)

If you’re starting gross anatomy – or know someone who is – what could be better than a felted liver in a glass jar? Shop owner yourorgangrinder also makes a brain, uterus, kidneys, heart, pituitary gland, lungs, and much more. So if you’ve got a favorite, she (or he?) is sure to have it. Happy dissecting!

Soap – Red Escherichia coli in a Petri Dish – Natural Honey Scent ($7)

Last semester in my research seminar class, we did a series of antibiotic resistance experiments. Good times, let me tell you. And let me also tell you that CleanerScience’s bacterial colonies look real, in terms of the streaking pattern. (Our colonies were off white, not red, but I’ll allow for artistic license in terms of color choice in the soap.) Super cool. And pretty ironic, to be using a bacterial plate as soap. I love it. What a scientific sense of humor.

Plush Mossy Chiton ($16)

Chitons are present-day creatures that look totally historic. We learned about them in Bio II, and looked at a preserved specimen in lab. This guy – made by LaBaleine – is pretty cute, if you ask me. And what a piece of history! All done in felt. Awww …

Neuron Necklace ($19)

I was trying to go for diversity in my listings, but I had to include two necklaces. This neuron necklace by Anatomology is so cool, and a great price. Just check out that axon and those dendrites. Just don’t wear it to your neuro exam … the professor might think you’re cheating.

Baby’s First Microbiology Book ($41)

When you first see the price of this book, you might think to yourself, “Well, I should just buy Baby a real micro textbook, for that price!” But don’t be fooled. This cushy, yet crunchy book has several felted pages of actual microbiology-related concepts. Hooray for science! Next time a friend – maybe even a stranger – has a baby, I’m totally buying them one of these. It’s that awesome. VerdantViolet also makes baby “textbooks” on nuclear physics, neuroscience, and other such topics.

Periodic Table of the Elements Women’s Sneakers ($83)

The last thing I need is another pair of shoes. I’ve got dozens, literally. But these nifty printed Keds, by juicygems, are rad. In the Radon sense. (If you didn’t get that chemistry pun, Google search an image of the periodic table and scan it until you find the symbol “Rn.”) I’m drooling over them. In the frothy H2O sense.

the Punnett square dominates ($1.50)

What can you buy for a buck-fifty these days? Not much. But beanforest sells these nifty buttons that allow you to show your support for the Mendelian genetic ratio at a great price. Turn it into a frig magnet for just fifty cents more. Cool beans.

Chemistry Crayon CLEAR labels – set of 120 ($15)

Here’s another way to expose the kiddies to science. Specifically, chemistry. They’re going to color, right? With QueInteresante’s stick-on crayon labels, they’ll inadvertantly be exposed to chemical compound names and formulas too. He-he-he. So tricksy.

Amoeba and Paramecium Felt Magnet Pair ($16)

These guys are fast swimmers when you view them under the microscope! I have quite fond memories of watching them squiggle, squirm, and pseudopod their way through their environments. These frig magnets by whatnomints are a fun, abstract reminder of those times.

Knitting in Biology 101 dark cork background ($95)

If I’d had the money, I totally would have bought aKNITomy’s frog dissection piece for my biology lab instructor from last year. I think she would have gotten a huge kick out of it. It looks so real! Even has those flat-head stick pins.

Pipette Tip Earrings with Red and Yellow Flowers ($10.50)

As my lab supervisor, Olga’s, PCR expert, I spend a good part of my day pipetting. So when I found these pipette tip earrings, I did a double-take. I gasped. Then I laughed. This is such a creative, fun gift idea for the lab worker. Heck, for anyone who likes research science. I’m going to buy a pair. Unless someone buys me a pair first. *Hint hint!*

Look At The Lab!

I took a few photos this morning of the lab where I work, just for the heck of it. I thought people might like to see the environment. Enjoy!

My workstation
Tools of the trade: ice, pipettes, tubes, my notebook. 

The chemical stock cabinet … look at all the goodies in there!