Debbie Knight

Archive for January, 2011|Monthly archive page

Working with “hot” stuff

In observation on January 25, 2011 at 1:51 pm

So tomorrow I will be working with radioactivity (or “hot” stuff, as we like to call it in our lab).   One of my lab mates is doing an experiment with an extended time course (over days) with some time points taken around the clock.  I get the afternoon shift.

The experiment will look for potential proteins expressed during an HIV infection that could be targeted by antiviral drugs.  And as awesome as that sounds, we will be working with quite a bit of radioactivity to track those proteins.

By the way, the symbol above is what we use in the research labs to designate that radioactive materials may be in the room and that certain rules must be followed while in that room.

When I first started doing research (many, many moons ago), there were few alternatives to using radioactivity.  But today, there are a plethora of substitutes that give a signal nearly as good as radioactivity does.  And this is true of this particular experiment, but my boss and his collaborator feel using radioactivity will give the best results — so, that’s what we’ll do.

I’m not opposed to using radioactivity in an experiment — and in some cases, there’s just no better way to get data.  It’s just that I prefer not to use it if alternatives are available.

If one works with radioactivity in a safe manner, there is little danger of harmful exposure.  And many safeguards should be in place, such as using the appropriate shielding (which in some cases is a thin piece of plexiglas).  Latex gloves, lab coats, and safety goggles are also safety precautions that should be used.

The key to working with radioactivity is understanding not only the safety rules  (like how to handle material safely and how to prevent a spill), but understanding the particular radioisotope you are using (like what shielding you will need and  how you detect it) are important as well.

So, do I get nervous working with the stuff — sure I do.  With radioactivity,  I need to be extra, extra careful and that can be a little tense at times.

The “fun” part comes at the end of the experiment, when you have to do surveys to ensure that there is no radioactivity in your working area, or on the floor, or on the lab door knobs.  This can take some time to do, but it’s necessary. You don’t want any radioactivity “walking” around the lab.

And that has happened — not to me, but to a lab mate a few years ago.  He got radioactivity on his shoe, which he discovered when using a survey meter doing a routine survey.  He had to put his favorite sneakers in a bag until the activity (in the radioactivity) had gone away — which took about five months.

Hopefully nothing like that will happen tomorrow.  So far I’ve worked with radioactivity without major incident.  But all the same, wish me luck!

A glimpse into research…sort of…

In observation on January 21, 2011 at 4:29 pm

A great video giving a glimpse into the research world (sort of…)  “borrowed” from YouTube — a science-related parody of the Lady Gaga song “Bad Romance.”

Over the years I have had my share of “bad” projects.

Projects where the experiments just aren’t working, where I spend more time beating my head against the proverbial wall than celebrating success.

Sometimes the breakthrough simply means trying a different approach.  Then the “bad” project blossoms into a “good” one.  Data begins to flow and life is good.

But sometimes nothing seems to work and the “bad” project is either put on the back burner or completely abandoned.

While a “bad” project can be quite frustrating, the challenge of flipping it into a “good” project can be rewarding — like solving a NY Times crossword puzzle in ink.

The “N” word…

In observation on January 19, 2011 at 11:01 am

I was sitting at my desk today when I overheard an investigator and his research associate discussing an experiment in the hallway.  They were talking about a immune cell found in blood called a monocyte. The investigator, who we’ll call Dr. A, told his associate that a receptor (we’ll call it “Z”) was never expressed on monocytes.

To be honest, I’m not sure which of the many thousands of receptors a cell can express on its surface they were specifically discussing. But what caught my ear was that Dr. A used the “N” word in the biology world:  NEVER.

(I also thought I may have heard a collective “gasp” from the biomedical community.)

In all my years working in a biological research lab, this word (along with other words that convey absolutes such as “always” or “forever”) are rarely uttered. Most scientists are trained to soften their statements to words such as “typically” or “seldom” or “frequently” or “most likely” or…well, you get the point.

Why?  Seldom are biological findings so definitive – especially when you’re talking about human beings.  It takes years and years of experimentation, testing things in many ways,  using different approaches and looking at things from many angles, before biologists can be relatively certain (ah, “relatively,” there’s another “soft” phrase used in the science world) that the phenomenon they have observed is real – that 1 + 1 really does add up to 2.

I argue that unless Dr. A has looked at every single monocyte in the human body — from many human beings, healthy and unhealthy, old and young, men and women — he could say with certainty that receptor Z is never expressed on monocytes.

I would also argue that if Dr. A had said it is unlikely that receptor Z was expressed on monocytes, their conversation would have gone unnoticed and I wouldn’t be writing about this at all.  So, thanks, Dr. A, for generating this little “discussion” about the “N” word.

Working together…

In observation on January 12, 2011 at 12:22 pm

I overheard a conversation between two researchers this morning while I was in the parking garage elevator. It was clear to this eavesdropper that they knew a little about each other’s research but not much. Most of the conversation on the ride down from the sixth floor was a general exchange of pleasantries.  During the course of that brief conversation, one researcher admitted he didn’t have any contact with the clinical side like the other researcher did.  By the time they reached the ground floor, they were making arrangements to discuss working together on a research project.

In the science world and, especially at a university, that’s called “collaboration,” and, ideally, that’s how science should work.

The university setting is a great place to establish collaborations. I’ve seen it happen quite a bit over the years.

Many of the collaborations happen between researchers within the same department.  Departmental meetings and seminars where researchers share their current work  provide ample opportunities for scientists to discuss how they could help each other out or what problems they might have had to overcome or that they need help in overcoming.

Collaborations between researchers in different university colleges (each made up of several related departments) have become increasingly commonplace at the university where I work.  Engineers working closely with architects or medical doctors or agricultural researchers are a few examples of the interdisciplinary research that can happen.

My husband, who is a biologist, works with a chemistry professor on how the chemical composition of the really small dust-like particles (or nanoparticulate material) that make up air pollutants affect biological systems  (such as human beings). When they first started this collaboration, there was a steep learning curve for each of them.  The biologist had to learn what the chemist was really saying (and vice versa) before they could make the collaboration work.  After several years of a successful collaboration, they have little trouble with communicating across disciplines.

Collaborations are the ideal, scientists freely sharing information with fellow scientists. However, in the dash to get grant funding and to have their work published  first in scientific journals, many scientists have become fiercely competitive.  Publishing your discovery before any one else can “scoop” you is the status quo these days — but that’s a topic for another day.

When things are working well, collaborations happen. And that is, in my experience, the way science should happen:  scientists helping scientists, for the good of science and mankind.

Yes, it’s a bit idealistic, but over the years I’ve seen both scenarios.  And  so far the unofficial result is that more can be accomplished by working together – ideas as well as results.

I wish the two researchers from the elevator good luck in forging a collaboration and keeping the spirit of science alive and well!

Hello, World!

In Uncategorized on January 10, 2011 at 12:06 am

Allow me to introduce myself and explain what this blog is about.

I’ve worked in biological research labs at two universities for over 20 years — primarily studying viruses.  Meanwhile, I’ve kept my eyes and ears open and learned about science and how science works — as an investigation as well as a business.

I started out as a lab technician in an environmental research lab at Purdue University.  The research group was  trying to find bacteria (or a group of bacteria) that could degrade agricultural pesticides.  What I found was a bug that could degrade aniline (which is simply a ring of six carbons (called a benzene ring) with an extra little NH2 stuck on it — a wee bit of a challenge for a microbe to break open but the form that many pesticides degrade down to and stop).  What was unique about this microbe I dubbed DAK 3 is that it could use this ring structure as a source of “food” even when there was plenty of glucose (table sugar) around.  Typically, microbes are rather lazy — they’ll use the easiest “food” source around, which in this case would be glucose.  Other than a manuscript published with my name included in the list of authors, nothing much came of this discovery.

A couple of years later, I moved to another state and began my career as a research associate at a another university in a virology lab .  The first skill I had to learn (and at first I had a difficult time wrapping my head around this idea):  instead of wanting the bacteria to grow in culture, the goal was to avoid bacterial contamination in the mammalian cell cultures.  The photo above shows me at the culture hood, surrounded by all the flasks that were used to make a stock of virus.

Over the  past 20 years, I have studied:

  • how a virus called cytomegalovirus (which is related to the herpes simplex virus that causes cold sores) hides from the immune system,
  • been on the ground floor in the discovery of an anti-viral drug (against cytomegalovirus) that has shown some promise in organ transplant patients,
  • discovered this same drug is effective against several other unrelated viruses, such as respiratory syncytial virus (RSV — which causes a lot of problems in newborn babies) and the polyomavirus BK-virus (which causes trouble in kidney transplant patients),
  • studied how HIV might pass from an HIV-infected mother, through the placenta, to infect a baby while it is still in the womb
  • how a rare neurological syndrome (called Susac’s Syndrome) may be caused by antibodies that recognize the cells that line the blood vessels (called endothelial cells) causing damage in the brain, eyes, and ears.

I’ve seen firsthand how the National Institute of Health (NIH) budget can affect research as well as careers.

I’ve worked with many research and medical scientists as well as graduate students, medical students, and undergraduate students.

In this blog, I hope to share these experiences.

And who knows, maybe somewhere along the way, you’ll learn something you didn’t know about the ins and outs of science.  No agenda — just what it’s like to be a “lab rat.”