Debbie Knight

Archive for April, 2012|Monthly archive page

Out for blood

In observation on April 26, 2012 at 9:00 am

I stumbled across this ad for research volunteers while waiting for the elevator in my building.  While the ad could use a little graphic design, this is a pretty standard posting for around the medical campus.

But I want to point out the way these vampiric researchers describe the volume of blood they will be drawing. Cups. Like measurements we would use in the kitchen. Kind of gross.

Maybe it’s just me, but I find it a bit distasteful to use “cups” and “teaspoons” when referring to bodily fluids.

These researchers don’t use those terms in the lab — we usually use liters and grams in the research setting.  In the lab setting “100 millilters”  has meaning, but outside of the lab? So it’s become standard practice to use kitchen terms so that everyone can understand, including people who don’t work in the lab.

It all goes back to the rules and regulations we have to follow when using humans in our research.

Most scientists don’t run around, jabbing random people with needles to collect blood without what is called an “approved human subjects protocol.” (I say most, because I’m not sure what some scientists do on in their free time, especially if they’re, say, a vampire)

This protocol can be a real pain in the assay to write up and get approved by the institution review board. The devil is in the details, as they say.

Everything has to be put in terms a high school student could understand. This is reasonable, but sometimes I think the review board members forget that today’s high school student may be more sophisticated than they think a high school student is. (Thank you, Internet)(oh, and teachers, too). 

And sometimes it’s quite a challenge to distill a scientific protocol in terms simple enough for that hypothetical high school student (I know, I attempt it here in this blog all the time)

And you need an approved protocol just to collect one tube (oops! I mean a tablespoon) of blood from a volunteer. Strike that. Make that a consenting volunteer (there’s a pile of paperwork to fill out, too!)

It may not sound like it, but I’m totally “for” having these rules and regulations, it protects the Henrietta Lacks of the world. Yes, there was a time, when medical researchers may have toed the ethical line (or even stepped over it — way, over it). And hopefully, with these rules and regulations in place, it really is a thing of the past.

The rules and regulations ensure that research with humans (and animals) is performed safely and ethically.  The term “ethically” covers a multitude of issues, including exploitation, discomfort, morality, etc.

I understand all this.

But do we have to use “teaspoons” and “cups” when describing bodily fluids?



Photo of the Week

In photo log on April 24, 2012 at 9:00 am

This is a poster (slightly customized) that hangs in my lab. It was “designed” during a time when we did quite a bit of work with viruses. And the only way to figure out how much virus there was in an experiment was to do a “plaque assay.”

The way we did a plaque assay was we added a solution with virus in it to some cells that were growing in a tissue culture plate. Let it incubate for an hour or so, so that the virus could attach and enter the cells before we washed off any virus solution that didn’t get in. Because this virus tended to blow up the cell when it was ready to spread to other cells, we would add a layer of agarose/media (think cherry jello) to the cells.  This “jello” fed the cells (the media part) and held the virus in one area (the agarose part). This forced any newly made viral particles to infect only neighboring cells and not the entire cell layer. After several cycles of blowing up cells and infecting neighboring cells, a “hole” was made in the cell lawn — we call this a plaque.

When the plaques were big enough to see with a low-power microscope (called a dissecting scope), we “fixed” the cells/virus in place with a solution of formalin. This killed the cells/virus and allowed us to stain the cells and count the plaques.

A plaque assay to count the amount of virus in a solution. The cell monolayer is stained with the dye crystal violet which turns the cells purple. The "holes" or clear areas are areas of viral infection. This image was borrowed from

For large experiments, it wasn’t so fun to count plaque assays — you might say it was a pain in the “assay.”  Hence the poster.

Science news stories need better context

In observation on April 19, 2012 at 9:00 am

I’m taking a science communication class this quarter. And one of my fellow students, a communication major, contributed the following to our class discussion:

“It only takes one gene to cause lung cancer. One day you’re smoking a cigarette when you’re 25 (years old), and one gene flips over and you’ve got lung cancer. It only takes one.”

It’s not quite that simple…

I didn’t say anything to correct him during the class discussion — but maybe I should have.

And it took me a while to realize how he might have arrived at this oversimplified and somewhat  inaccurate conclusion.

News stories often report that scientists have discovered yet another gene associated with some form of cancer. Important information to relay, but without the proper context, a reader could think that it only takes that one particular gene with a single mutation to cause cancer when in reality it’s an accumulation of changes in the cell’s genome.

And it’s complicated.

Scientists still think it takes multiple assaults to a cell (especially to the DNA) before that cell becomes cancerous. Each of those assaults can cause a small change which by itself has little if any affect on the cell.  But those assaults start to add up (like cars in a multiple-car accident) and the chaos that is cancer can ensue.

The assaults can be many things (chemicals, sunlight and radiation exposure come immediately to mind). And those assaults can affect the cell in a variety of ways. It can affect the DNA, how it’s expressed, how the gene product interacts with other gene products, etc. A mutation in the DNA which changes one letter in the string of letters of a gene could change the way the blueprint is interpreted into a protein. The addition of a group of atoms (like a methyl group, for example) can interrupt where the blueprint-reading machinery hooks up to the gene’s promoter changing how that gene is expressed. Some assaults affect the proteins made from those genes. If a protein is made wrong it can change how a signal is transmitted from outside the cell to inside the cell. But not all involve an actual gene — it can occur in the DNA sequences between the genes. Pieces of DNA can switch places with other pieces of DNA which can occur within a single chromosome or between two chromosomes. And with the discovery of micro-RNAs, things have gotten that much more complicated.

Pretty much anywhere there is some form of cellular control there is vulnerability.  And the list is extensive.

A person can even inherit DNA from his parents that has a few of these changes already on board. This means that although these inherited changes may not cause the disease, it may take fewer assaults for this individual to develop cancer.

For example, a woman may inherit a mutation in her BRCA1 gene that puts her at higher risk of developing breast cancer but that doesn’t mean as soon as she’s born or hits puberty that she will have breast cancer. It may take a few more DNA changes before a cell rages out of control to become full-blown breast cancer. On the other hand, there is a possibility, based on the rest of her genome, that the woman may never develop breast cancer in her lifetime.

As I said, it’s complicated.

So, the student was not entirely right when he said it only takes one gene to be “flipped over.”

It is a single step (in a series of steps) in the making of a cancer cell.

And it doesn’t stop once a cancer cell has finally lost control of itself. More assaults, more mutations, more changes can make the cancer cell grow faster, help it dodge the immune system or help it escape to other places in the body.

I realize that in a news story there is limited time and space to discuss all the angles, but an effort should be made to include perhaps a tiny paragraph that places the discovery and the risk in  proper context.

A few well-placed words could prevent a misconception like this student had.


Additional reading:

Baudot A., de la Torre V., and Valencia A. Mutated genes, pathways and processes in tumours. EMBO Rep. 2010 October; 11(10): 805–810

Stratton S.R., Campbell P.J., and Futreal P.A.  The cancer genome. Nature. 2009 April 9; 458(7239): 719.

Photo of the Week

In photo log on April 17, 2012 at 9:00 am

This is a photo of a gas regulator we use in the lab. We hook it up to a tank of compressed carbon dioxide to control how fast the gas flows into our culture incubators. Too much or too little of the gas and the cells will die.

Every couple of months, I have to whip out the biggest wrench I’ve ever worked with to change the gas tank. Sometimes I even have to hang on the wrench to loosen the nut between the regulator and the tank. I’m sure that’s a sight to see.

But I’m sure an even funnier sight is me wrangling the unwieldy empty gas tank to another room. It ain’t pretty.

The delivery guys can spin two of them at once (full ones, so they’re heavy).

They make it look easy.

It’s not.

A Day in the Life: April 12, 2012

In research log on April 12, 2012 at 10:00 am

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 on a particular day. These entries I will call “A Day in the Life…”

We had a little kindergarten-style show-and-tell in our lab meeting today.

Usually we bring pieces of paper showing our data all neatly graphed, but the chemical engineering graduate student literally brought his experiment with him. The vials were passed around for all to see.

He brought them because he wanted to discuss the experiment, how the experiment looked and what should happen next. I must say it felt a little strange to see the vials out of the lab setting. But it was equally cool to see the results rather than just hear his verbal description of what the product looked like.

Vials from an experiment. Before the experiment (left) the contents look "milky." And after the experiment (right)? The contents still look milky but now some stick to the sides of the vial.

Photo of the Week

In photo log on April 10, 2012 at 9:00 am

One of my favorite parts of protein analysis is making a solution of sodium orthovanadate (NaVO4).

When I add a little hydrochloric acid (HCl) to the solution, it turns yellow (photo on far left). As the solution comes to a boil, the yellow fades to clear (left to right).

That’s the part I like — the color change!

For those who want to know what’s going on at the chemical level, I have to say I’m not a chemist. But the person who trained me in this procedure told me the color change was because the “ortho” in the orthovanadate changed to another form. I looked it up online. Three sources stated this is done to activate (depolymerize) the orthovanadate so it’s better at its job — which is to prevent certain enzymes (phosphatases) in the protein extract from munching on certain parts (phosphate groups) found on many proteins in a cell.

Perhaps I’m easily entertained, but watching for the moment when the color changes never gets “old” — even after the 247th time!

Unfair advantage at science fair competitions?

In observation, research log on April 5, 2012 at 10:09 am

Andrew and I planning his experiment.

I found this photo in an old shoebox. This was in the early days of my career and my boss had “volunteered” me to help a junior high school student with his science fair project. It’s been a long, long time, but I think his name was Andrew. His mom took the photos in this post as “proof” that he worked on the project. And if I recall his project won at the local science fair competition and he went to regionals with it. I don’t remember how he placed there.

Even after 20 years, I remember that his project looked at how a chemical called salicylic acid (which has analgesic and anti-inflammatory properties and is used in acne medications, etc.) effects the cells that line the blood vessels. These cells are called “endothelial cells”  and my lab worked with them quite a bit.

If I recall, we treated the cells with different concentrations of salicylic acid and looked at the effect on a few proteins that the cells expressed on their cell membranes. To look at those proteins, we used antibodies that recognized those proteins, tagged them, and looked for the signal on a flow cytometer. (Now, tell me, would he have thought of this project all on his own?)

So, I taught Andrew how to add the chemical to the cells, how to prepare the cells for flow cytometry, and how to run those cells on the flow cytometer.

I remember that none of the latex gloves we had in the lab fit his small hands — it was like he was wearing floppy socks on his fingers. I’m not sure how he managed, but he made do.

Andrew running his samples on the flow cytometer, with some assistance from me.

I also remember I was a bit conflicted as to whether this was “fair” to the other science fair participants. (and I still am)

Here this kid is doing an experiment in a bonafide university lab, with lots of help from me and my boss.

Did he think of this project himself? No.

Did he design the experiments himself? No.

Did he perform the experiments himself? Not exactly. I was hovering, ready to swoop in to help at a moment’s notice.

I felt in a way it was cheating — he had an unfair advantage over other participants who designed and performed their own experiments in a home “laboratory” (i.e. a kitchen or garage).

Sure we were building and nurturing his interest in science. That’s always a good thing in my book.

I’m just glad I’ve never been a science fair judge because I’m not sure I could be impartial to the kid who clearly did his project all on his own with no help from a mentor. The project that isn’t so fancy-shmancy but shows the promise of a budding scientist. The underdog.

Nowadays, it seems pretty commonplace for serious science fair participants to be mentored by a research scientist.  Just look at this year’s winners of the Intel Science Competition. The grand prize winner looked at molecular mechanisms that might slow cancer cell growth — he clearly didn’t do this research in his garage.  The same could be said about the third place winner who isolated and mapped a gene.

The science competition allows students to work with a teacher, an academic scientist, or an industrial professional. While I admire the science the students present, the cynic in me can’t help but wonder how much of the idea and designing the student actually  did on the project and how much the mentor did.

Is this practice “fair” to those students who have the interest and drive to do this level of research but don’t have the access to such facilities? Is is okay for kids to do their science fair projects in a research lab? Should the science fair competition organizers limit the amount of outside help a student receives?

While I struggle with these questions, I will stop and wonder how Andrew turned out — is he a scientist? Did this experience influence that choice? I have not idea, but I certainly hope it did.

Photo of the Week

In photo log on April 3, 2012 at 9:00 am

My department has a shared resource: an ultra-low temperature freezer which sits alone in a shared lab space. Last week I wandered into this space and noticed the digital temperature readout light was out.

Hmm, that’s strange, I thought.

I instantly regretted opening the freezer door.  I found the freezer had stopped working. And judging by the amount of mold, mildew, and fungus “fur” growing on the sides of these freezer boxes, I’d say it stopped working quite a while ago.


I’ll give you one guess who had to clean out this freezer.

If you guessed the “finder,” you’d be right.

I considered breaking out a hazmat suit before embarking on this little cleaning “adventure,” but I opted for gloves and a mask instead.

The boxes went straight into a biohazard box. I wasn’t about to look inside those boxes to see if the contents were possibly biohazards — I figured the “fur” on the outside qualified them as such. I then proceeded to disinfect the inside of the freezer.

This certainly will go down as one of my least favorite lab experiences!

The March 2012 Top Five List of Amusing Search Engine Terms (that found Biologyze)

In observation on April 1, 2012 at 8:18 pm

With March Madness nearly over, I thought I’d recap the top five search engine terms (that I found amusing) used to find Biologyze in March.

#5: is polio virus bioterrorism scary
Um, while many viruses with the right “training” could become a bioterrorism threat, there are better candidates for the job (in my opinion).

 #4: how many dart tests do you run after autoclave fixed
What? Dart tests? Do you throw darts at the autoclave and if it lands squarely in the bull’s eye, the autoclave is deemed “safe to use?”

#3: inside of autoclave chamber is blue
Clearly people are having some issues with their autoclaves. This problem sounds more like an April Fool’s joke, the autoclave is preggers or it’s the result of a well-mounted Smurf attack.

#2: thinking cap guinea pig
So wait, is the thinking cap made of guinea pig? Or maybe the thinking cap is for the guinea pig’s head? Will a thinking cap even work on a guinea pig? Is putting a thinking cap on a guinea pig considered animal cruelty? I’m not sure I want this person visiting my blog any more…

 #1: tritium burn through dry ice and car video
Huh? Tritium can’t even penetrate a piece of paper – how the heck is it going to get through a barrier of dry ice and car?

So there you have it.


Runner’s Up:

ice statues drink

how do run flat tires work