Debbie Knight

Archive for November, 2012|Monthly archive page

A Day in the Life: November 14, 2012

In A Day in the Life, research log on November 14, 2012 at 3:51 pm

From time to time, I will give a glimpse into the “glamorous” life of a research associate and talk about what I’m doing in the lab. These entries I will call “A Day in the Life…” 

This week I’ve been burrowing through scientific journal articles, ferreting out information that might help move my research project along. We, in the scientific community, call this a “literature search.” And my work is starting to pay off. So far, I have found one really solid lead that I may pursue.

While I was searching the scientific / medical article database called PubMed (maintained by the National Center for Biotechnology InformationU.S. National Library of Medicine), I noticed a cool feature that I hadn’t seen on this site before. There was this little chart (a histogram) that tells you how many articles were published each year on your topic of interest.

This is useful in that it tells you whether you’re looking at a “hot” area of research. Or what years the research was hot.

For example, I typed in the term “immunoglobulin and complement fixation” and saw this chart:

So in 1973 (the first bar on the left) there were 643 articles published. If I scroll back a few years, the research actually peaked in 1971 with a whopping 730 published articles.

And in 2012? (the bar on the far right) A measly 15 articles. Obviously not the hotbed of research it once was.

When I searched “immunoglobulin subclass,” I got this result:

I’m not sure what was going on in 1990, but that seems to be the peak of this topic’s publication, maxing out at 267 articles.

And when I typed in “nanoparticles” (a relatively new area of research), I got this:

Last year, there were an incredible 11,756 articles published on this topic. Talk about “hot” area of research! This dwarfs the previous two searches. And I’m sure that number will continue to climb.

I was amazed there were two articles on nanoparticles published in 1978.

I’m not sure when PubMed added this feature. Admittedly it’s been a few months since I searched for articles. But I like it.

Photo of the Week

In photo log on November 13, 2012 at 1:44 pm

Yes, this is a picture of a lab shelving unit.

Boring?

Perhaps.

I certainly thought so, too, until a soon-to-retire professor told me the story behind it.

Apparently the black soot on the side of the shelving unit was the result of a lab fire from years ago.

Someone had stored ether (a highly flammable substance) in a refrigerator. Enough ether evaporated to fill the refrigerator compartment so when the compressor kicked on early one morning: ka-boom!

The refrigerator door blew off.

Flames shot everywhere.

The fire department was called.

And there was quite a bit of damage to the lab.

Luckily, it was early enough in the day that no one was working in the lab, thus no injuries.

The professor’s story certainly makes this boring old shelving unit just a little more interesting. At least to me.

A reminder (to me) why I blog

In observation on November 9, 2012 at 10:00 am

Wow.  As a blogger, I often wonder if what I write is reaching anyone.

I’m sure this is something with which many bloggers struggle.

Today I got a comment on a blog post from July. “A reminder (to me) why I do research” was about a heart-rending email my boss received from a patient.

The comment, which I will place here anonymously, was equally heart-rending.

Here was another woman with a clearly debilitating medical condition, searching for answers to her medical mystery. And she stumbled onto my blog, presumably through an Internet search.

One line from her message gave my heart an extra twist: “I have no health insurance but the ER.” (Wow, that’s something I take for granted in my own life.)

Another gave me hope because she has people who really care for her:  “I have family willing to take me anywhere or do anything to help me.”

She wrote:
 “I am convinced I have Susac’s Syndrome. I have cotton wool spots, terrible chronic headaches, personality disturbances, hearing loss, confusion, memory loss and vision loss. My MRI is normal. … I have no health insurance but the ER.

“I read what you just wrote here and I was wondering, can you tell me what kind of specialist I should be sending my pleas for help? I have family willing to take me anywhere or do anything to help me. I just don’t know where to start.”

In an email sent to her privately, I will give her a name of a clinician with whom we collaborate. I hope he can give her sound medical advice and an idea where to start unraveling her mysterious illness.

Good luck, SZ! I hope your journey of discovery will lead to your restored health!

Photo of the Week

In photo log on November 8, 2012 at 4:15 pm

A new office mate was unpacking his desk. One of the items was the molecular biologist’s “bible” also known as “Current Protocols in Molecular Biology.” My lab has one of these as well – although we haven’t kept it current with the subscription which offers periodic updates. So, I guess you would call ours a “Not-so-current Current Protocols in Molecular Biology.”

Our meager three-volume set dates back to the early 1990’s. A lot has changed in the world of molecular biology since then. We subscribed for a couple of years, but it was a real pain in the buttocks to insert the updates (which sometimes involved removing existing pages).

Despite its outdatedness, our set is still useful.

It not only offers tried and true scientific protocols, but also gives good background on the techniques (like why you add reagent Z after reagent A) and troubleshooting tips (like why adding reagent Z before reagent A is not such a good idea).

I’ll admit  I rarely use this handy reference.

I often turn to commercially-available kits for much of my molecular biology needs.

Case in point, my new office mate relayed the following hallway conversation he had recently. (For simplicity, the office mate we’ll call “Dude-1” and the person from a neighboring lab “Dude-2.”)

Dude-2: Do you know how to clone a gene?
Dude-1: Sure, I know how to do that, but I haven’t done it in a long time.
Dude-2: What kind of kit did you use?
Dude-1: Kit? I didn’t use a kit. I made all the reagents myself.
Dude-2: Oh. Um. Well, thanks any way.
Exit Dude-2 as he walks to the next (and hopefully more “hip”) lab seeking his answer.

A subscription to “Current Protocols in Molecular Biology” isn’t cheap.

According to the website, it now costs $1200 for a new one-year subscription to the six-volume set and $650 to renew. And keeping up with the times, there’s also an online subscription rate for labs: $550 per year.

For smaller labs running on a shoe-string budget, this subscription rate (whether online or hard copy) is cost prohibitive. This might explain why we haven’t had a subscription for many (many!) moons.

A Day in the Life: November 2, 2012

In A Day in the Life, research log on November 2, 2012 at 12:57 pm

From time to time, I will give a glimpse into the “glamorous” life of a research associate and talk about what I’m doing in the lab. These entries I will call “A Day in the Life…” 

Yesterday’s experiment  didn’t go so well.

And it wasn’t even really my experiment. My lab was helping out a newly-hired pathologist get some data that he could possibly use in a grant proposal.

We treated some cultured cells (specifically ones that line blood vessels called endothelial cells) with a potential cancer drug. This drug may work to treat brain tumors in two ways — directly on the tumor cells and on the blood vessels that supply nutrients and oxygen to them. We treated with several doses of the drug for different amounts of time. We stained the cells for a couple of things that would show us if the drug concentrations were toxic to the cells.

To look at those markers, we used an instrument called a  flow cytometer. This machine slurps up the cells floating in a buffer solution and marches them single file past a laser beam and a series of sensors. One of those sensors counts the cells. Ideally we would count 10,000 cells, but the samples were taking a long time to run. We settled on counting only 5,000 cells — more than enough to get valuable information from the other sensors.

Some samples took only a couple of minutes.

Not ideal, but I could live with that.

But some samples took a lot longer. And some never reached the 5,000 cell mark. For example, the cytometer had only counted 3,375 cells in six minutes and 28 seconds in this particular sample (the highest dose of the drug). Argh!

It was very frustrating.

It  was also a little boring watching the samples run.

To keep myself busy (and entertained), I read a journal article, perused the school newspaper, outlined experiments that I needed to do, doodled, took some photos with my cell phone for this blog, worked on a crossword puzzle, checked my cell phone, crunched the results that slowly trickled in, etc.  I also used the data as a Rorschach test (of sorts), trying to see if I could “see” anything in the data. 

Rorschach test? What do YOU see?

The first set of samples (of a total of six sets) took two hours to run. This was all at top speed on the cytometer, mind you. The proverbial pedal was to the metal.

It was then I made an “executive decision” to run only two of the three samples per treatment. This, I hoped, would give me adequate data.  And I wouldn’t be running my samples, one at a time, manually for 12 hours straight.

It only took half that time!

Six.

Long.

Hours.

No lunch. No break.

Sometimes that is a day in my life.