Debbie Knight

Archive for July, 2012|Monthly archive page

Luxury lab equipment not always an option

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

A sales flyer was slipped under my lab door by a sales rep from a scientific supply company.

This happens from time to time.

But what caught my eye was the “PCR Plate Spinner” ad with a sale price of $449.

This is probably an excellent price for this piece of lab equipment.

For those of you wondering what the heck a “plate spinner” is: it is a motorized contraption in which you put a plastic plate that has 96 little “cups” (or wells) built into it. Liquids that you put into these little cups can cling to the sides, so you use “centrifugal force” to collect those little droplets at the bottom of the cup. (For “centrifugal force,” think amusement park ride where people are strapped into a large rotating drum. As it spins, people are smooshed against the outside wall. In some versions, the floor drops out in the middle of the ride and the people stay stuck against the side. This is what we call “centrifugal force” — the quotation marks are there because this force doesn’t really exist, but that’s more of a discussion for a physicist than a biologist).

The lab in which I used to work had a more economical way to spin their plates to collect all the liquid in the bottom of the cup: they used a salad spinner equipped with rubber bands to hold the plate in place. A salad spinner that you could get at any local retail store or even a garage sale. Cost: between $1 – $20.

Besides the cost savings, this “home-spun” version can save time. You can spin four plates at one time (rather than a single plate in the spinner from the scientific supply company).

A win-win!

(not that I’m saying I’d pass up an opportunity to have the luxury electric-powered spinner)

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A Day in the Life: July 30, 2012

In A Day in the Life, research log on July 30, 2012 at 5:53 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…”

There is a piece of equipment (a film processor) in our lab that is available to anyone in our department to use. In the past several years that it’s been in our lab, I have never had to post a sign that says “Please keep this area clean!” … until today.

Either a yeti has come through and trashed the area. Or the personnel from the only lab currently using this equipment is the culprit. I’m betting on the people since I haven’t heard of any yeti sightings in my building.

And, yes, you can probably tell I’m a little peeved by this turn of events.

It is a major break in laboratory etiquette to go into someone else’s lab, use a piece of equipment and leave the area a mess.  If done more than once, you risk losing the privilege of using it. Simple enough. This isn’t my rule. It’s just common sense and common lab courtesy.

I posted the sign with hopes that these people will take the hint.

But I’m a little sad that I had to post it in the first place.

(sigh)

My Name’s on WHAT?!

In observation on July 25, 2012 at 3:04 pm

Today, the blog “Retraction Watch,” reported the retraction of a scientific research article from the journal Cell Biochemistry and Function. 

They included this excerpt from the retraction notice written by the editors of the journal:

“The following article from Cell Biochemistry and Function, “Notch activation Is regulated by interaction between hCLP46 and the chaperone protein calnexin” by Xiaoqin Feng and Lixin Liu, published online on 3 April 2012 in Wiley Online Library (www.wileyonlinelibrary.com), has been retracted with agreement from the authors, the journal Editor, Nigel Loveridge, and John Wiley & Sons Ltd. The retraction has been agreed because the paper was submitted without approval from the co-author, Lixin Liu, and contains data that requires further experimentation in order to support the conclusions fully.

What? The paper was submitted without approval from the co-author?

I can tell you from my own experience that it happens.

And it’s easier to do now than it used to be.

Back in the day, most journals required that every author physically sign the submission form before the editors would accept a manuscript for review.  And sometimes it was a big pain in the buttocks to collect all those signatures (I know. I often was assigned this task). Of course I would look at published research with multiple institutions and oodles of authors and feel sorry for the person(s) who had to collect all those signatures.

Nowadays, manuscript submission is a little easier. Most journals use a digital submission process. And while I honestly don’t know the submission requirements of every single scientific journal, I do know that this signature requirement has eased somewhat.

Case in point: one of our collaborators included my name as well as my boss’s name on a paper she submitted.  No signatures were required. In fact, we had absolutely no idea she submitted it until we got an email from the journal that the manuscript had been received and would be reviewed.

What?!

We scrambled to get a copy of the manuscript to see just what it was about, how our data had been used in the report, and whether we supported the conclusions she had made.

While it may seem a windfall to have your name just “show up” on a published paper, the truth is: it’s not. The fact your name appears on an article implies you participated in the research process and you fully endorse the reported findings.

Scientific reputations are on the line.

In this particular case, it turned out okay. She drew the appropriate conclusions.  So we let it ride. And the paper was published. Of course, that doesn’t mean we were happy about it. Nor does that mean it was ethical of our collaborator to put our names on the paper without our knowledge.

(Note: This particular collaborator is now a former collaborator because of other unethical behavior (see post). I guess the incident describe above should have sent up a red flag, but it didn’t. Live and learn.)

Photo of the Week

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

Last week a guy came by to inspect our fume hood.  He checked for things like adequate air flow.

He also left behind a new placard on the fume hood glass sash reminding lab personnel that leaving the sash in the closed position is not only safe (you know, in case of malfunctions) but it also saves energy (the ventilation system that pulls air up and out of the hood doesn’t have to work as hard when the sash is closed).

So, he placed it in an obvious place — the center of the glass, near the bottom of the sash.

A good idea?

Well … maybe not.

What he hadn’t considered is that when the sash is in the “up” position — when someone not as tall as he is working in the fume hood — the sign is right in the line of sight, blocking the view into the hood.

So now what are we supposed to do when we’re doing experiments? It’s not really safe to work with stuff while ducking to look under the glass pane — the glass pane is there to help prevent chemicals from splashing in your face. And it’s not really safe to work in the hood while standing on a step stool — a falling hazard. So it looks like I will have to try and relocate the sign. It’s stuck on the glass like a bumper sticker — strong glue and everything. I’m not entirely certain the sign will make it through the removal process.

I like the sign.

I like what it stands for.

But it’s going to have to move.

Photo of the Week

In photo log on July 19, 2012 at 10:30 am

One of my tasks in the lab is parceling reagents into smaller portions. We in the research lab call this “aliquoting” — a word that the Merriam-Webster dictionary recognizes as a legitimate word. Who knew?

It’s a rather menial task, but there are times I welcome doing it. It gives me time to think — sometimes about an experiment and sometimes about non-science stuff. The task does require a little focus, so full-on daydreaming is out of the question.

And, the best part is: when the task is complete, there’s a sense of accomplishment.

A day in the life: July 17, 2012

In A Day in the Life, research log on July 17, 2012 at 12:36 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…”

So, this week I am learning how to separate proteins by their overall charge. The technique is called isoelectric focusing. It seems like a complicated procedure, so for the moment I’m willing to accept this as a mystical process. As I gain experience working with the technique, I will understand more of the science behind it.  But for now: black box.

I like to learn new techniques. It keeps me on my toes.

So, I’m learning this technique because I have been using Western blot analysis — a procedure which only separates proteins based on their size. I need to find out if what I’ve been detecting is one specific protein or a pile of proteins that just happen to be the same size. One way to determine this is to separate the proteins first by charge, turn the strip 90 degrees, and then separate the proteins by size. So you’re essentially separating the proteins in two dimensions.

Separating proteins by charge. The biggest hurdle for me was figuring out if I was going to do this technique “old school” which apparently nobody does any more (and there’s probably a good reason it has fallen out of fashion). I know one person (my former boss) who has done this technique with thin tubes of glass (called capillary tubes). I have the equipment in the lab to do the technique this way, but everything I’ve read says it is not as reliable as using pre-made strips (new school). Given that I don’t want to spend all my time banging my head on the wall trying to figure out why my experiment isn’t working, I opted for the more reliable “new school” way of doing things.
(Note: this doesn’t mean I won’t be banging my head on the wall, but hopefully it will be for less time)

The next thing I had to do was find a researcher who had the equipment to run these strips and who was willing to let me use it. I used my professional network to find someone.

Then I had to buy a bunch of reagents which I could have spent a couple of days making. Okay, this is where experience comes in. While it might look like I was opting for convenience, I was trying to maximize my chances of success. If I made any one of the reagents I needed incorrectly, it might take me several experiments before I figured it out.

So, I started the experiment yesterday, kits and strips and instruction manual in hand. Seemingly simple: you put your samples in a tray, place the strip over it, and let it incubate overnight. Trouble came in the form of bubbles in my sample — which according to the instruction manual are your enemies. I think I won the battle, but time will tell.

Today I will actually run the samples on the equipment.

And, tomorrow, I’ll find out if it worked.

I’ve got my fingers crossed that it will work! But just in case, I’ve got a couple of consultants on speed dial.

A Day in the Life: July 13, 2012

In A Day in the Life, photo log on July 13, 2012 at 3:16 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 reading up on how to do a complicated protein separation method (called 2-dimensional gel electrophoresis). I will be attempting one of these next week and want to make sure I have everything I will need to do this technique.

One of the things I will have to do for this method is to concentrate the amount of protein I have in my samples. I will use a kit that will pull the protein out of the liquid sample (by precipitation) which will allow me to put it in a smaller volume of a different liquid solution.

In all my twenty (plus!) years as a research associate, I have never seen an instruction manual for a kit tell me which way to orient the sample tubes in the centrifuge.

“Position the tube in the centrifuge with the cap hinge facing outward.”

This is one of those things that is usually left out of a protocol. Something you have to figure out on your own. Or a “trick” you learn from another lab member.

Well, that and the magic incantation you must repeat three times while hopping on one foot!

Photo: Where microwave popcorn comes from?

In observation, photo log on July 11, 2012 at 9:00 am

This is a photo from my archives. Taken maybe 22 years ago.

Yesterday, I posted a photo of me standing next to a ground-water well in the middle of the soybean field. Well, THIS is what I drove past on my way back to that well.

This is a REAL photo, not altered or “Photoshopped. ”

Now, I’m a city dweller, not used to the sights of agricultural research. I’m sure these bags were placed over the tops of these plants to prevent something like cross-pollination between plants.

But you’ve got to admit it looks a lot like the farmer was growing microwave popcorn.

Photo of the Week: Outstanding in the (soybean) field

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

This photo is from my archives. Taken over 20 years ago.

This is me standing at a (then) newly-drilled ground-water well in the middle of a soybean field in West Lafayette, Indiana. The self-portrait was taken back when I first started doing scientific research as a career.

I would use the removable  attachment (and tubing) to pump out two or three knee-high glass carboys which were pretty heavy when full. I would lug them back to the lab for our experiments.

The water was used for three purposes.

One was to look for microorganisms in the water that could degrade pesticides that were applied to agricultural fields. (This was my part of the project)

Another was to look for signs of breakdown products of the pesticides as they percolated through the soil and bedrock down to the aquifer. (This was the soil agronomist’s part of the project)(Oh, if you ever want to yank an agronomist’s chain, just refer to soil as “dirt,” they LOVE that!)

The third was to slowly pump the water, with its load of pesticides, through a column of soil that we had in the lab. The soil, as all soils do, had microorganisms that flourished with very few added nutrients. By subjecting them to the pesticide-contaminated water, we hoped to select for microbes that could break the pesticides down into simpler molecules, using the energy that came from the chemical bonds to grow. We would frequently test the liquid that came out of this soil column for microbes and for breakdown products of the pesticide. (This was a graduate student’s project that I helped sometimes helped with)

It was really weird standing in the middle of a soybean field, alone, pumping out water to the crackling of the high-power lines and the buzzing of insect wings.

One of the many weird things I did for this project in our quest to find microbes that could break down pesticides. (More on these later)

A reminder (to me) why I do research

In observation on July 5, 2012 at 9:00 am

My boss received a heart-rending email from a woman who may have the disorder we are studying in our lab: Susac’s syndrome.

This syndrome is thought to be caused by damage to the tiniest of blood vessels (the microvasculature) in the brain (especially in the corpus callosum, a band of fibers that allows communication between the two halves of the brain), in the inner ear (which can cause hearing loss), and in the retina (which can cause vision loss). Because the symptoms do not always occur at the same time, it is difficult to diagnose Susac’s syndrome. In many cases the syndrome resolves within a few years, but not without leaving behind permanent damage. Steroid therapy sometimes helps slow its course, but there is no real cure at this time.

She wrote:
“I have seen numerous doctors and done numerous tests. I think I have done every lab test at least two, maybe three times. I get daily headaches, body aches, and I am having trouble concentrating, spelling, and reading. I have two boys that are both very physically active, and I used to be able to keep up with them. But that is even a chore anymore. I’m only 41, and this just isn’t me. It has been a very difficult year. And it has affected work and is starting to affect my marriage.”

She goes on to ask if we will test her blood to see if it behaves similarly to patients with confirmed cases of Susac’s syndrome.

What she is looking for are clinical test results, something that we cannot give her because we are a research lab and there is, as yet, no approved diagnostic test for Susac’s syndrome. We are not sanctioned to perform a clinical test on human subjects.

We expressed our sympathy and invited her to participate in our research by sending us a blood sample (with a signed consent form). But that is about all we can do for her, except continue searching for biological answers.

I admire her “take-charge” attitude, seeking answers to her medical mystery. I’m sure I would do the same thing in her situation.

But I hope she is wrong. I hope she doesn’t have Susac’s syndrome but instead has something simple to treat and easy to resolve.

In the meantime, I will work even harder on this research with the renewed understanding that there are very real people out there, with very real symptoms that have profound effects on their lives.