Debbie Knight

Archive for May, 2012|Monthly archive page

Data sharing in collaborative research not always easy

In observation on May 31, 2012 at 9:00 am

A problem that comes up when two or more labs collaborate is how to share the data with the group … beyond the lab meeting.

This issue came up in our meeting today.

We had a system of writing up summaries of the week’s results and sending them to one of the professors to archive. This was supposed to be what he called “a living document.” But the problem is that the information goes to him but is not easily shared amongst the group.

The research has grown and we need a better way to share the data and other information.

We do not have a group website at the moment, not do we have the time to build one at the moment – we’re too busy doing experiments and keeping up with the science literature to build one.  So that option is “out” for the moment.

There is something called an “electronic lab notebook” which is essentially a website that allows people to share information. It allows people to upload not just data, but PDF’s of journal articles that are relevant to the data entry (like where the experimental design came from) or information about the materials used in the experiment (like lot numbers, expirations dates, how many times the reagent has been frozen and thawed, etc.). The amount of content that can be put in these entries is unlimited since it is online.

The beauty of these electronic lab notebooks is they are searchable – just enter a key word and all the entries that contain that word are brought together. You can compare what reagents were used in experiments that worked and compare them to what didn’t work – perhaps a reagent has lost its potency over time. It might become obvious when comparing these experiments side by side.

Sounds great, so what is the problem?

It’s the cost to subscribe to the service and to maintain the service. These are, after all,  replacements for the hardcopy lab notebook. So if you don’t pay to maintain the service, I’m not sure what happens to those records. Are they gone forever?

While the electronic notebook seems a good solution for our problem, money is tight so we will have to look at more economical ways to share our data.

After much discussion we have decided to try Google Docs to share the data and relevant scientific literature. This sounds like a good low-budget option for our needs. Although we will have to bring at least two of the professors up to speed on how to use Google Docs — you know, bring them into the 21st century.

We’re going to try it and see how it works. (I will let you know in a later update)

If any of you readers have had a similar problem and have found a solution, by all means, please share your suggestions. Your input would be most appreciated.


Photo of the Week

In photo log on May 29, 2012 at 9:00 am

This is a photo of some Scrabble tiles (with magnetic tape) that we have on the side of our lab freezer.

I had an old Scrabble game where the board was water damaged, but the tiles were perfectly fine. What to do, what to do.  I got the idea to put magnetic tape on the back of the tiles in an effort to re-purpose them so that my labmates and I could have some nerdy fun.

Here’s our most recent construct.

A Day in the Life: May 24, 2012

In research log on May 24, 2012 at 9:05 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…”

Today was moving day, of sorts.

I am fortunate to have a desk in a shared office space. If I didn’t, I would commandeer bench space in the lab or a desk in the hallway.  The worst of these three options is the in-the-lab desk because you cannot eat or drink food in the lab (or at your desk).

Luckily, I didn’t have to move out of the office. but four large desks did. They will now live in a new office space with the department’s accountants. (I’m not sure in which office they’d have the most fun, but I’m betting it’d be ours)

So, I spent most of today and earlier this week packing (and unpacking) many of the desks.

I’ve also been helping a new faculty member who will arrive in the fall. He has a rather extensive list of equipment that he will need for his lab. I’ve been tasked with sifting through equipment in two formerly occupied labs, finding some of those items on that list. And then,of course, moving it to the space that will be his lab.

Both tasks have made the week very “exciting,” let me assure you. But that’s life in a research lab sometimes.

Photo of the Week

In photo log on May 22, 2012 at 9:00 am

Lab safety manuals, training documentation and other lab records all neatly filed in a row of three-ring binders. Obviously I had some fun designing the binder labels.

While I sometimes complain about how much we have to document in the research lab, I am eternally grateful that I don’t have to document as much as clinical labs do.  The photo below was taken a few weeks ago in a lab that does genetic testing. The walls in several of the lab’s rooms were lined with shelves and shelves of three-ring binders, each containing patient data. The clinical results have to be saved for at least five years in the lab.

One small shelf three-ring binders. This clinical lab had shelves and shelves as well as rooms and rooms of these binders filled with patient results.

Want a glamorous lab job? Try out this one!

In research log on May 17, 2012 at 9:00 am

A tub of dirty dishes.

Whether those dishes are found at home or in the lab, they generally sit there until someone takes the initiative to wash them.

In our lab, since we have to wash them by hand (rather than in an automatic laboratory dishwasher that some research buildings have), we usually wait until the tub is overflowing with dishes (as this one is) or when we need something that is in the bin. It’s not a matter of neglect, it’s a matter of how busy we are designing and performing experiments. We don’t have the luxury of having a paid undergraduate student employee to do this task.

And I admit, there are times when I purposely ignore the growing collection of glassware trying to out-wait my lab mates as to who will wash the dishes this time. (Shhh! It’s our little secret)

Dishwashing is not a glamorous task, but it is nice when you want something mindless to do.

Here’s how we do it in our lab.

So, a laboratory staple when it comes to dishwashing is a detergent called “Alconox.” We could use regular dishwashing detergent like you find in the grocery store, but this one leaves less residue on the glassware — important in the lab setting since we re-use these bottles to make various lab solutions and culture media. Any soap residue might adversely affect those solutions and the experiments in which we might use them.

Alconox, an iconic laboratory detergent

We use a bottle brush to scrub out the glassware, especially the bottles. We have a couple of sizes of bottle brushes. One looks like something the Jolly Green Giant would use for his dishes. The one in the photo is a more manageable size.

Bottles are scrubbed out with a bottle brush

After all the bottles have been scrubbed, they are rinsed several times with tap water and then several times with deionized water. We do the final rinse in deionized water to remove any impurities that the cheaper tap water might have left in the bottle.

Rinsing out the suds with tap water

After all the dishes are washed, there is a sense of accomplishment. You have a drying rack full of clean dishes …

… and, more importantly, an empty bin!

An empty dish bin is a lovely sight

Photo of the Week

In photo log on May 15, 2012 at 9:00 am

This is a typical hallway in a research building, one lined with research posters.

These posters were designed to show data from some aspect of research going on in the lab. Nearly all of them have been to a local, national, or international scientific meeting in an effort to share and discuss that research with other scientists.

But once the meeting is over, what do you do with the poster? Sure you could roll it up and store it in a file cabinet. Or you could  put it on the wall outside the lab to show your lab neighbors and passers-by just what is going on in your lab.

Science, despite the stereotype of isolation, really is a social affair. It’s about sharing results, ideas, and discussions. And displaying research posters is just another way to promote these activities.

Besides, you’ve got to put something on those bare institutional-white walls, right?  Why not something we scientists have plenty of — data?!

Brain picking parties, all the rage

In research log on May 10, 2012 at 9:00 am

Warning: this post is not for those who are easily grossed out.

I stumbled across some old photographs of lab days gone by and thought I’d share them with you.

Back in the day we would have “brain picking parties.” And they were all the rage … sort of.

One of many brain picking parties we held in our lab.

The day would start with me going to the meat packing plant to pick up four or five cow brains. Gross, I know. But we needed the growth factors that the brains had in them.

I remember the first time I went to the meat packing plant, I was more than a little disturbed by the sides of beef moving past me on hooks, knowing that a few minutes ago those sides of beef were part of a living, breathing (and probably freaked out) cow.

I wouldn’t eat beef for quite a while after these trips to the plant.

Over time, the meat packers told me that due to tightening safety regulations they would no longer be able to give me the brains. Apparently it was rather dangerous for them to open the bovine skulls (I envisioned a sharp ax, but I’m not sure what they used). However, they did offer that I could take a couple of cow heads to the lab with me … but with visions of The Godfather flickering in my mind, I declined.

We found another source of cow brains – a private butcher. This meant I had to drive an hour each way to get these brains, but it was worth it. However, this place looked like someone’s ranch home gone house of horrors. I couldn’t leave quickly enough from this place. Yikes!

And eventually this source dried up as well.

I’m actually glad because that means we now buy bovine brain extract commercially. It’s not as cheap as buying cow brains at $5 each, but at least I can sleep nightmare free these days.

So, why did we need cow brains? The brain is full of fantastic growth factors that made our cultured endothelial cells (which were isolated from the blood vessels in discarded human umbilical cords) grow like gangbusters. Without the growth factors, the cells simply would not grow when we isolated them.

Making this brain extract was a tedious process, taking days to make, so my lab and another lab who also grew endothelial cells would come together for these “brain picking parties.”

One of our larger brain picking parties.

The most tedious part was removing the outer membranes from the brains – hence the “brain picking” part. And as you might imagine, all sorts of off-color comments and jokes would fly around the lab bench as we removed these membranes (called “meninges”).

We would work with only small portions of the brains at a time. We had to work quickly and keep them chilled because as warmed up in our hands, they would get a bit soft as the fats in them warmed and became more, well, gooey.

A beaker full of "clean" brains

I always found it amazing that this brain, that easily fit in the palm of my hand, had been the thought and coordination center for a half-ton (or more!) animal. I wondered what it had been thinking, feeling, dreaming before its untimely demise.

A younger me, passing out some brains

We would weigh the cleaned brains, put them in a Waring blender (a staple in many a lab) along with some ice-cold saline and make (as we called them) “brain shakes.” These “shakes” were a foamy pink concoction – they didn’t look appetizing in the least. We would pour the blended mixture into a large glass flask that was kept on ice as it stirred for two hours.

"Brain shakes"

Anything that was not extracted was removed using a large centrifuge.

The fats were precipitated out of the solution overnight and removed by centrifugation.

More centrifugation and then the brain extract was placed in small glass bottles which were swirled furiously on a shaker as they were frozen in a dry ice bath. This froze the extract on the sides of the bottles to increase the surface area when we put them in a machine called a lyophilizer. Basically, this machine was a large sealed bin that used a vacuum pump to pull a vacuum. As the contents of the glass bottles warmed up and melted, the vacuum would draw out the water, leaving behind a freeze-dried brain extract. We would then put on lids on the bottles and store them in the freezer until they were needed.

So after two long work-intensive days (and then some waiting), we had our homebrewed bovine brain extract which we treated like gold.

Of course now, with the threat of bovine spongiform encephalitis (or mad cow disease), we would have to do things a little differently.

There you have it. The “good old days” of life in the lab.

Do you like to blow stuff up? This could be for you.

In observation on May 9, 2012 at 10:01 am

blow stuff up ad

Saw this sign posted in the Chemistry Building this morning and I just had to share it with you.

What it lacks in design, the sign makes up for in phrasing because it certainly caught my eye. I’m not a chemist, but I sure want to sign up for this!

I especially like the disclaimer: Explosions vary by semesters. Void where prohibited.

Photo of the Week

In photo log on May 8, 2012 at 9:00 am

Most labs in my building do not have plants growing in their labs. This is because the soil can contain bacteria, fungus, molds, etc. that can contaminate a biological experiment.

This lab has chosen to grow some plants in the hallway. It’s a nice pop of color in an otherwise beige world — at least in this hallway.

I wonder how long it will take the vines to creep down to my lab (across from the yellow safety shower head).

A day in the life in a Entomology Department?

In observation on May 3, 2012 at 9:00 am

Professor Rhineholdt? I think I found the experimental subjects you lost

I visited a friend who started working recently in the entomology department. The department is housed in is new building, so imagine my surprise when I saw several bug traps scattered about the floor and on his desk.

What? How can there possibly be an infestation of this magnitude in a new building?

Oh, wait, they study insects in an entomology department. So these bug traps were to capture runaway test subjects. I get it.

I can just imagine a big hissing cockroach sauntering past the pencil sharpener. Or a dung beetle taking up residence in the chairman’s “in” box. Or a swarm of fruit flies taking off with someone’s lunch.

I don’t think I could work in the entomology department. I think I would only want to see insects out in nature, in a documentary film, or behind the glass in an enclosure — not skittering across my computer monitor. Eeeek!