Debbie Knight

Archive for April, 2011|Monthly archive page

Dust bunnies fill the void in an empty research lab

In observation on April 29, 2011 at 2:40 pm

Her lab now stands empty.

She was not a tenured faculty member which left Dr. T quite vulnerable. Her job security (and eventually her salary) depended on her ability to support her research. She was never able to secure much grant funding – maybe little grants here and there, but nothing substantial like a NIH grant. Her research looks at some very specific proteins produced by a human viral pathogen. Perhaps it was the extremely narrow focus of her studies or that her work did not translate easily into medical science, I can’t say.

And after several years of struggling to keep her research going, the departmental chair made the tough decision to let her go.

For the moment, she has landed on her feet. She had been collaborating with another researcher, a surgeon who doesn’t have much time to devote at the research bench. And he is able to support Dr. T for a single year which has led to an unconventional working arrangement. He will be her supervisor (at least on paper) even though she has more research experience and training than he does. She will work on getting the preliminary data that they will need for grant proposal submissions. If they are unsuccessful, it is unknown what her fate will be.

So, this week was moving week.

She had professional movers lug much of her lab equipment to another building. So now all that is left is in her lab, besides dustbunnies, are an odd assortment of test tube racks, glassware, and plastic ware as well as abandoned equipment that may or may not function as they once did.

It’s a little sad to see her go. Her fiery personality definitely kept things interesting around here. But knowing that she is still doing research offers some cheer.

I wish her luck – better luck than she has had so far. And hopefully her luck will change in her new research environment.

Perhaps I should have given her a lucky bamboo plant…

Federal funding lull a bit too much reality for a first-year graduate student?

In observation on April 21, 2011 at 2:30 pm

One of the research projects I work on involves a biology team working with chemistry and chemical engineering teams. And we have weekly meetings to share our results.

Last week, the meeting was more organizational in nature than results reporting, and it turned to how difficult it is to get grant funding in our respective fields. Not the happiest of conversations these days.

And at this meeting was our first-year rotating graduate student (the only student at this particular meeting) who sat quietly listening to this depressing conversation. At one point, the chemistry professor acknowledged we probably shouldn’t be talking about this topic in front of the student because it was discouraging. I agree. But being a pragmatist, I think it’s probably a good thing for her to hear it sooner rather than later – it’s a serious reality for scientists right now.

The conversation eventually turned to planning experiments for a grant proposal submission in June – a happier and more hopeful discussion.

I asked the graduate student afterwards what she thought of the funding situation we discussed. And she quietly said, “It’s really scary.”

She hadn’t been aware of  the funding funk before she started graduate school eight months ago.  She had only heard a little about it during her rotation last quarter.

So, here we have a first-year graduate student, committed to the next four or more years to getting a PhD, with this looming cloud hanging over her bright future.

As a research associate, I depend on grant funding for my employment. And I’ve been around long enough to see some bad times in the funding situation, times where I sweated over whether I would have a job. But those lulls have never been this bad or lasted this long before. In the past, the pendulum has swung back to better funding opportunities – not quickly, mind you, but they did return to reasonable levels.

And I’m hopeful it will happen again – though I don’t think it will be happening in the next year or two. Without a crystal ball and not knowing how long before things begin to get better, it’s difficult to tell the student that all will be better by the time she graduates. I certainly hope it has. Or we both might be looking for a new kind of job!

NPR video communicates science creatively

In observation on April 18, 2011 at 2:15 pm

The link to this NPR video came across on my Twitter feed yesterday. And I think this is a great way to explain a complicated scientific experiment in a simple-to-understand (and fun) format. Maybe more scientists (and science communicators) should consider alternative and creative ways to make science more approachable to the general public.

Kudos to NPR’s Robert Krulwich and Odd Todd for putting this together!

Here’s the original Science article titled, “The ant odometer: stepping on stilts and stumps.”

A Day in the Life…April 14, 2011

In research log on April 14, 2011 at 5:34 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 on a particular day. These entries I will call “A Day in the Life…”

A  couple of weeks ago, we got a frozen vial of cells from the American Type Culture Collection (ATCC) – cells that were isolated from a colorectal cancer that we will use to model the lining of the intestines. Not a perfect model, the cells are, after all, cancer cells which means they’re different from the original cell type in several ways – they have mutations in their DNA, they may have more than the standard 46 chromosomes in the human cell, and they grow more quickly in culture than their original counterparts, but hopefully they will behave enough like the original cells that we can draw meaningful conclusions from our experiments.

So, in that frozen vial we got from the ATCC is perhaps a million cells – though it sounds like a lot, it’s not quite enough for our research needs. So, we have to place them in a small tissue culture flask, allow them to grow and crowd in, and then transfer them to more tissue culture flasks. We will repeat this a few times to further expand the culture.

Our cells look something like this when you look at them under the microscope. (This image taken from

Since this is a new cell line for us, I’ve been freezing a small portion of the culture at each transfer. We do this primarily in case our culture becomes contaminated with bacteria or fungus – not something we want to happen, but it can occur. If the culture does become contaminated, it’s nearly impossible to get rid of it so it’s best to discard the culture. By freezing some cells at each step, we ensure that we have a few cells saved for future experiments.

So, we store the frozen cells in a cryopreservation tank. Remember the scene from the movie “JurassicPark” when the guy who’s stealing the dinosaur embryos takes them out of a “steaming” container? Well, in the movies they probably used dry ice or a fog machine to achieve the “steaming” effect, but in the research lab, we use liquid nitrogen to keep the cells frozen. The “steam” actually looks similar to the “fog” produced by dry ice or the fog machine and a little like steam from boiling water.  The “steam” from liquid nitrogen is not warm at all, in fact it’s quite cold. Liquid nitrogen boils at minus 324 degrees Fahrenheit – brrr!

So, when you freeze the cells, you can’t just put the cells in the liquid nutrients (culture medium) you’ve been growing them in – if you did that, the ice crystals could pierce and shatter the fragile cells. To prevent the cells from rupturing during the freezing process, we add a commonly used chemical called dimethyl sulfoxide (DMSO) at a concentration of 10% just before we freeze them. There are more elaborate cryopreservatives that we could use, but DMSO is cheaper and works fine for our needs. We are able to thaw the cells on a later date, most of them will remain intact and grow.

So, now we have millions of cells stored in our lab making it possible to do many experiments in the future.

Cryopreserving cells is one of the things I did today in the lab – not the most exciting thing, but definitely an important task.

A Day in the Life: April 13, 2011

In research log on April 13, 2011 at 3:26 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 on a particular day. These entries I will call “A Day in the Life…”

Today, I’m delving into the scientific literature, searching for ways to isolate and culture cells from the intestines. There are quite a few journal articles out there – which is good, this suggests it is possible to culture these cells on a long term basis. It also suggests that despite the fact that the intestines are teeming with bacteria, an “enemy” in the tissue culture world, that intestinal epithelial cells can be cultured without the bacterial contamination.

One journal article had an isolation protocol that sounded promising – only the details of that protocol were in another article the authors referenced. (Okay, this happens quite a bit, I can follow the paper trail.) So the reference in turn referenced another article for the protocol. I had to dig through a total of six references to find the original article that actually described the protocol – a record in my experience!

My question is: Why didn’t the first article I found simply reference the original article – the one that actually described the protocol? Why put the reader through all that?

I’m thankful that my mentors showed me a better way to write a journal article. They taught me to reference the original article. And they also taught me to give a brief description of the protocol in the methods section. I think that’s a good thing – I know I appreciate it when I’m on a literature search.

Okay, back to the journals…

Repair or Replace? Adventures with wheelbarrows and broken-down lab equipment

In observation on April 13, 2011 at 11:38 am

For a week, I’ve been trolling hardware stores, home improvement stores and Internet sites looking for replacement handles for my (formerly) trusty wheelbarrow so that I could get some yard work done. Ultimately, I was able to find the exact handles I needed, only I would need to buy a new wheelbarrow to get them (apparently, the handles aren’t sold separately at retail stores). I didn’t really want to buy a new wheelbarrow because, with the exception of the rotted wooden handles, the wheelbarrow was in good working order. A seemingly simple thing to fix – except I couldn’t find the parts anywhere and I have no way to do my own woodworking. So, I finally broke down and bought a new wheelbarrow. I still hold out hope to fix the old one, but I had work that could no longer wait.

This experience made me realize (again) just how “disposable” American society has become. There isn’t even supporting infrastructure to repair rather than replace broken equipment. And it’s no wonder the landfills are filling up – they could be overflowing with broken-handled wheelbarrows!

In the academic research setting, there seems to be a little bit of infrastructure to aid in repairs.

Lab equipment (as simple as a research-grade blender or as complicated as a gas chromatograph with mass spectrophotometric capabilities) is quite expensive and many researchers will make a valiant effort to repair the equipment before buying a costly replacement.

If they’re lucky, they have a service contract held on the equipment, so a service call can readily fix the problem. Of course, those service contracts usually cost a few thousand dollars, so not every piece of lab equipment can be covered.

Some labs and departments cannot afford such contracts. So in those situations, and if they’re lucky, there’s a mechanically-inclined person in the lab or down the hallway who can figure out why the equipment is no longer working.

Sometimes, the manufacturer has parts available, and sometimes they don’t. In those cases, you might have to come up with a “creative” repair solution (for those who ever watched the TV show “MacGyver” would understand what I mean by “creative” – the guy could fix anything with a paper clip and duct tape).

The creative solution could add years to the equipment’s lifespan or it might just work long enough to get you through the next experiment or two until a more permanent solution can be found.

Perhaps we all could learn (or re-learn) a lesson here. Perhaps we could think twice about running out to the retail store to replace that broken toaster or blender. Perhaps an attempt to repair could be made before the appliance is heaved into the old landfill where it might ultimately end up next to the broken-handled wheelbarrow.


The Dance: The Graduate Student and the Lab Rotation

In observation on April 5, 2011 at 5:09 pm

Let me start by saying that unlike the character depicted in the comic above, I actually love the lab I work in as a research associate and would fully recommend working here to anyone who asks.

That being said, we have a first-year graduate student rotating through our lab this quarter. This will be her fourth and final rotation before she decides on a lab in which to do her dissertation work.

She already has an offer to work in the lab in which she rotated during Fall quarter – which means she impressed a difficult-to-impress researcher enough for him to offer her a position in his lab before she left for another rotation. It has to make her feel great to already have a solid offer. (It also suggests she might be a great addition to the lab in which I work.)

She was more impressed during her Winter quarter rotation – so much so, she would love to remain in the lab for her dissertation work. Unfortunately she is competing with at least one other student for the position in the lab and because her competition is rotating through that lab this quarter, she won’t know if she has an offer until June.

So, while she waits to hear from this lab, she is rotating in our lab.

With grant funding so rare these days, graduate students in the program are cautioned only to rotate in labs that have adequate funding to support their dissertation research. And we have the funding to support a graduate student who is interested in nanoparticulate research. (So put out the word!)

Nanomaterials are used in a lot of products, but we do not know how safe those materials are. (I wrote about this on a previous occasion.)

It’s a new project and it’s off to a slow start.  While we are wait for some newly purchased tissue-cultured cells to grow so in sufficient quantities to use in experiments, our rotating student has been reading scientific journal articles.

Not the best first impression, I will admit. But hopefully the project will take off soon – and she’ll have more than enough to do during her rotation to get an idea if she’d like to continue working here.

So, you may not know much about lab rotations. A lab rotation is not only a time for the lab to evaluate if the student will be a good “fit,” but also for the student to determine if they like the research and the people in the lab – after all, this is where he or she will spend the majority of the next few years.

A good fit and everyone’s happy and research life is good.

A poor fit and….well, let’s just say, the student’s life can become quite challenging over the next few years. I’ve seen several promising graduate students who became so miserable in their lab setting that they chose to leave graduate school.  (This hasn’t happened in our lab, mind you!)

No one wants that to happen – hence the rotations.

I don’t know how things will work out this quarter – will she like the research enough to want to stay?  Will she be a good fit?

To be honest, it’s too soon to tell. But so far, things are going well. And whatever the outcome, I wish her luck and happiness in her future endeavors.

Recycling plastics in the laboratory setting

In observation on April 1, 2011 at 2:45 pm

It’s amazing how much plastic waste is generated in a biological research lab. First you have the disposable plastic pipets and pipet tips which allow for the accurate measurement of liquid reagents. Then you have the weighing dishes used to weigh out specific amounts of chemicals. And then there are the tissue culture flasks and dishes, petri dishes, centrifuge tubes, microcentrifuge tubes, reagent bottles, disposable cuvettes, syringes, etc. All of which are predominately single use items.

And most of these items come in some sort of plastic wrapping or containers in order to maintain sterility or purity.

So, the plastic waste can really add up.

It seems that most laboratories don’t even think to recycle some of the things they add to the waste stream. I know this because I see what they put in their trash cans and it makes me sad. Plastics as well as cardboard and paper can always be found in many trash cans dotting the hallways.

In my lab, I routinely collect the recyclable plastics that I can safely collect and place them in the recycle bin. I also reuse some of the plastics (like bottles) when I can.

In addition to recycling, there is more that can be done. Replacing disposable items with more enduring, reusable items can make a difference. My former boss, a young and enthusiastic researcher, made the conscious decision to use reusable glass pipets instead of disposable plastic pipets in the lab. Not only did it save some money in lab supplies, but it also reduced plastics in the general waste stream.

I won’t kid you, the glass pipets took some effort to reuse. They had to be decontaminated, washed, rinsed, dried, sorted, and loaded into metal canisters before they were sterilized and ready for another round of use.

I thought this was a great idea when I joined the lab. And I still do, even though I no longer work in this lab. But it’s not a perfect system. Some lab members would use the disposable plastic pipets whenever they were available – they were convenient.

The university recently started a recycling program to recycle pipet tip boxes which are made of plastic not routinely recycled by local recycling companies. I’m not sure how many labs are aware of this program because I would say tip boxes are the No. 1 item I see in trash bins.

Though sometimes I feel I’m on a one-person crusade, I do the best I can to recycle whatever and whenever I can.

Even when I walk down the hallway, if I notice recyclable items in a trash can, I often will place them in a nearby recycle bin. (I’ll note here that I’m not entirely convinced that the maintenance staff actually places those recyclables in the big recycling bin located on the loading dock – I suspect much of what is in the smaller recycling bins ends up in the general waste stream.)

Perhaps one day, the trash collecting companies will be able to sort recyclables from the regular waste stream, making separating trash and recyclables obsolete. Until then, I do what I can to help the environment – one recyclable item at a time.