Debbie Knight

Archive for the ‘Uncategorized’ Category

Leaving a mark

In Uncategorized on January 10, 2015 at 5:10 pm

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I was in our collaborator’s research area and discovered this little collection of empty champagne bottles – each signed by a graduate student on the day he or she had defended a Ph.D. dissertation or a Master’s thesis.

Many bottles also sport a sentiment in addition to a signature and defense date. The sentiment sometimes deep and meaningful, sometimes simply joyful.

My lab also holds this tradition.

I found this interesting that the tradition exists in other research environments — this one chemistry, mine biology.

I think it’s a great way of leaving a small mark that says “Yes, I was here!”

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Greener pastures for unwanted lab equipment ?

In research issue(s), Uncategorized on June 12, 2013 at 2:12 pm

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My department has had some faculty turnover. Some have retired. Some have found positions elsewhere.

This means there have been several labs I’ve helped clean out.  And I’ve seen quite a bit of laboratory equipment, much of it functional, taken to “surplus.”

Now in concept that sounds pretty good. You send stuff to a surplus warehouse where other labs can go and possibly acquire the cast-off equipment. The ultimate in recycling and reusing, right?

Well, the reality is that at my institution the surplus warehouse only takes office furniture and office equipment. The lab equipment is sent to the landfill – even if it’s functional.

When I found this out a few months ago, it was a major reality check.

I thought back to how many things my department has sent to surplus in just the last few months. Had I known, I would’ve tried harder to find a lab that could’ve used it.

So, this week, a faculty member who is moving to a smaller lab space said to me, “Oh, we’re sending that to surplus.” And he had absolutely no idea what it really meant. The landfill.

One of the items was a perfectly functional biosafety cabinet. (For those who don’t know what this piece of equipment is: it’s sort of a big metal cabinet with a filtered ventilation system that allows you to safely work with cells, tissues, viruses, and other possible biohazardous materials .)

I couldn’t see one more senseless disposal of an expensive piece of equipment. These things, new, can cost thousands of dollars.

So, I used my connections and managed to find it a new lab home.

I’m also trying to find a new home for a big floor-model centrifuge. I’ve had a couple of nibbles, but so far no takers. But I’m hopeful that I’ll succeed. Research money is tight and someone out there must need a centrifuge.

I wish there was a way to easily put functional lab equipment up for adoption at my institution. A centralized warehouse, a website, I don’t know.

And for the equipment that no longer works? Maybe that could be put up for adoption as well. It could be cheaper to repair broken equipment than to buy new.

Or maybe functional or not, unwanted equipment could be sold on eBay and serve as an additional source of revenue for my institution.

Update: Good news! Found a new lab home for the centrifuge. I may have cast my net a little too wide because I’m still getting emails from various labs saying they are interested in taking this centrifuge. 

The “core” of the problem?

In Uncategorized on February 14, 2013 at 11:16 am

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My department has some scientific equipment that is shared by all its members. I’m talking the pricey, big ticket items like flow cytometers and confocal microscopes that very few individual labs could afford.

It’s a great idea. And I actually wish that there was more shared equipment like centrifuges, for example. And maybe even some smaller, more affordable instruments.

But, alas, in a department that is spread out in five buildings, it’s nearly impossible to have truly communal equipment. Now, don’t get me wrong, most investigators are more than willing to let others use their specialized equipment.

The department actually has allotted lab space for the shared (or, as it’s called “core”) equipment. So the flow cytometer and the brand-new confocal microscopes are housed in a lab. There’s even a person who manages the area. Well, actually one and almost-a-half persons. The almost-a-half person is me.

In a new turn of events, there are members of the department who want to make the core equipment a fee-for-service deal. Where, if you are not a member of the department and you use the equipment, it will cost you. Not a bad way of earning a little revenue to help defray the cost of the equipment’s maintenance contracts which can run $2,000 a year.

I will tell you that the one and almost-a-half person staff are not as “expert” as we would need to be to actually run a fee-for-service core facility.

If I was paying to use the flow cytometer, I would expect the staff to help me set up my protocol and attempt to fix any problems that might arise while using the instrument.

Oh, sure, I’ve done my share of flow cytometry. But I’ve only done the simple stuff like looking at one or two fluorochromes (they “glow” when they are hit by the cytometer’s laser beam). But it gets really complicated when you’re looking at more than two because one fluorochrome’s “glow” might overlap with another’s. You have to make adjustments to how much of the flow the cytometer’s detector, well, detects. I haven’t done this. It’s something that I would need to learn.

The other staff member has never used a flow cytometer. Talk about a steep learning curve!

There exists a really good flow cytometry lab that is fee-for-service on my side of campus. They will even run your samples for you – if you’re willing to pay.

A really good microscopy facility exists as well. They may not scan your slides for you, but it is worth having these experts available to help.

In my department, the fee-for-service idea is just talk at this point, but I suspect it will happen.

That being said, I wonder if we “build” it, will they come?

Got a blunder wonder in the lab? There’s an award for that!

In Uncategorized on October 11, 2012 at 9:00 am

With the Nobel Prize going out to various recipients this month, I thought it would be appropriate to talk about the much less prestigious “Dumbass Award.”

Truth be told, I was rummaging around on my computer for a photo and I stumbled upon the completely forgotten “dumbass award.”

A relic of a former lab.

We had a pretty big lab crew. And we were a pretty jolly group.

I can’t remember the specific event that lead to the invention of this award, but one seasoned lab member made a truly rookie mistake that messed up her experiment.
(Please note: it wasn’t me)
This lab member was probably called something like dumbass.
(Yes, it’s not exactly politically correct, but we were a close group, we often referred to each other in such loving terms)
And then some jokester thought it would be a good idea to invent an award for the blunder wonder. Hence the birth of the Dumbass Award.

Let me first say that humans work in the lab. We don’t intentionally set out to make mistakes, but they happen. It’s easy to forget to perform an experimental step, forget to dilute a solution, etc.

Some mistakes are recoverable. Others are not.

But not all mistakes are bad. Sometimes it leads to a “eureka!” moment. Admittedly rare,  it can happen.

More often, the mistake will tank an experiment.

But it takes more than just your garden variety mistake to earn the “dumbass award.” For this award, it needs to be a stupid mistake that is typically witnessed by someone else. After all, no one in their right mind would willingly admit they did something to earn this “auspicious” award.

Receiving the award strongly motivated the awardee to find someone else who deserved it more. No one wanted the award, let alone keep it.

While it wasn’t created to do so, it improved lab efficiency to some degree. Perhaps it increased awareness.

I don’t remember why, but the dumbass award was eventually retired.
Perhaps the same people earned it over and over again.
(Yes, I might have been a recipient a couple of times)
Perhaps people moved on.

But for whatever reason, the award now sits on my computer’s hard drive. And I think I’m happy to let it stay there, reminding me to make every experiment count.

Besides, my lab mate didn’t seem too excited about resurrecting it.

Double, double, toil and trouble

In Uncategorized on October 31, 2011 at 5:01 pm

Happy Halloween, everyone!

Double, double, toil and trouble...

In honor of All Hallows Eve, I thought I’d cover a rather gruesome topic to those working in a research lab.

It can fill even an experienced researcher with dread. (Cue the sound of distant howling)

It can bring research to a screeching halt. (Cue the clinking chains and disembodied moaning)

It can drive a graduate student or a research associate to desperate measures. (Cue the maniacal laughter)

What could possibly be this “scary” in a research lab?  (Cue the creepy organ music)

The bane of the research scientist’s life — troubleshooting!

Take a beautifully-working protocol that suddenly won’t work anymore and the hours, days, weeks of troubleshooting that can follow can be quite a challenge. (One might even say horrific, at times).

It is especially troublesome to troubleshoot a time-consuming multiple-step protocol where any given step could be the source of the problem and it isn’t apparent there is a problem until the protocol is finished several days after it’s begun.

A reagent, a piece of equipment, a contaminant are but a few of the places a problem can arise.

If you want to truly appreciated how many things could go wrong at any point in an experimental protocol, just look at my post describing a protein analysis protocol called Western blot analysis.  Problems can occur at any of those steps described, from the isolation of proteins from cells through the detection of the protein on the blot.

Another lab technique that I’ve personally found vexing is nested polymerase chain reaction (nested PCR) which looks for specific genes or pieces of  DNA in a sample. This technique is so sensitive that the tiniest speck of contamination can give a positive result where there should be none. And result in hours and days of trying to figure out from where that contamination arose.

Determining just where the problem lies in an experimental protocol can be quite aggravating. It often requires a series of tightly-controlled experiments  to identify the source of the problem. And sometimes it just means starting completely over — making new reagents, opening new boxes of supplies, whatever else you might think of.

To be honest, there are times when getting a protocol to work again seems more “magic” than method.

If you’ve worked in a lab long enough, experience shows you that if you can get the protocol working again, whether you identified the specific problem or not, you accept that it’s back online and resume cranking out data. Don’t look back. Don’t ask questions. Just crank.

And the best part of this hair-raising tale: the scariest part is behind you — no more double, double, toil, and trouble. (Cue the birds chirping and sound of children at play)

At least until the next time. (Cue the dissonant note and return to melodic musical score)

An article on technicians

In Uncategorized on June 1, 2011 at 1:32 pm

I thought  “Lab personnel: Technically gifted” might be interesting to some readers. This article from Nature discusses the different levels of technicians that work in a labs and the future job outlook for them.

 

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.”