Debbie Knight

Archive for October, 2011|Monthly archive page

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)


A Day in the Life: October 25, 2011

In research log on October 25, 2011 at 5:36 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…”

Once a week, we have a meeting with our collaborators – a chemistry professor, two chemistry graduate students, and a chemical biomaterials engineer. (Sounds like the makings of a rather corny joke.)

While we communicate pretty well now, it did take a while for us (the biologists) to understand the chemistry side of things and vice versa.

One of the chemistry graduate students is preparing for his qualifying exam which involves writing a mock grant proposal and defending that proposal to his committee members.

So, Andrew presented his idea for his mock grant proposal. He wanted to get feedback from the biologists in the group – a biology professor, a research associate, and a graduate student. And he had some pretty cool ideas (which could even result in a real grant proposal). (Note;  I’ve known one graduate student whose mentor submitted her grant proposal to the National Institutes of Health and it was funded! Quite a spectacular feat for a graduate student and a great feather in her career cap!)

The chemistry graduate student managed to stump the biologists in the group for a few moments when he started talking about cancer cells and an enzyme they overexpress. The details don’t really matter here, but what does matter is that this chemistry student who synthesizes nanomaterials in the lab (pure chemistry) knew more about this enzyme (a biological protein) and its relationship with cancer biology than we did.

Now to give us credit, we aren’t cancer researchers. And what we do know about this enzyme, my boss and I learned  in passing — a mention in a journal article we were reading or a quick reference in a scientific presentation – nothing formal. The biology graduate student? She may have heard about it in one of her classes.

I’d also like to mention that my lab’s research covers a few human viruses as well as immunology relating to the viruses and to the nanomaterials. Our knowledge about cancer biology is not nearly as extensive.

But still!  A chemistry student showing up a biologist on his or her own playing field?  Tsk. Tsk.

We’re not proud! And we know we don’t know every last thing about every last thing. Which is good because this could have been embarrassing!

Score one for the chemistry graduate student! Good job, Andrew!

An open letter to those whose lab rotations are not going well

In observation on October 21, 2011 at 11:08 am

One of the perks of using is that it gives its bloggers information about how people find their blog. One of those parameters is what words  were used in Internet searches to find a specific blog post.

Yesterday one of those searches was “lab rotation not going well” which linked this person to my post called “The Dance: The Graduate Student and the Lab Rotation.” I will admit this post was probably not all that helpful to this particular seeker, but his or her search inspired me to write what I wish they would have found on my blog yesterday. Here is my response.

Dear “Lab Rotation Not Going Well,”

I realize you found my blog by accident when you typed “lab rotation not going well” into the Google search box.

And I realize that you probably won’t revisit my blog to see if I’ve posted anything new on this topic.

But let me tell you that your search touched me. I felt a deep sadness that you are not having the best experience during your rotation.

But all is not lost: think about all you are learning from this experience.

First, you’ve found out that it’s not a good fit with the researcher (a future mentor), his research, and you. That’s an important thing to learn during a rotation – you’re testing the waters to see if you can handle this mentor and the research project while you’re in graduate school. You’ve only committed to work in the lab for a few weeks and you can choose whether you’d like to join the lab should you be invited. You can escape this situation.

That’s great news!

I’ve known graduate students who have discovered long after they committed to their dissertation work that they are absolutely miserable in their mentor’s lab. At this stage in their graduate pursuits, they have few options. While a handful of students chose to stick it out, many have dropped out of their graduate program altogether or opted to get a master’s degree rather than a doctoral degree. It’s sad to see, but it happens.

So, you are way ahead of the curve!

Second, you obviously had some hope this rotation would work out well for you because you recognize it’s not going well. That hope may be there for several reasons. Perhaps the research focus is your favorite subject. Perhaps the research is cutting edge and exciting. Perhaps the researcher is famous and hitching your wagon to his star would help you advance career-wise. Perhaps you’re having a hard time connecting with the person you’ve been assigned to work with. In any case, it’s obviously not going well or you wouldn’t have performed your Internet search. Again, the good news is: there are other labs and researchers out there!

While I can’t begin to devine your specific situation from those five little words in your Internet search, I think I need to remind you that there are two people in this “dance”: the researcher and you.

An obvious place to start looking for reasons why this dance isn’t going so well is YOU. Ask yourself (and be completely honest here) what you can do to turn this around.

  • Is there something you’re not doing? Should you be doing more?
  • Are you not showing interest in the research? This one is the biggest deciding factor I look for when I’m working with a rotation student.
  • Are you just showing up just when you have to? Are you staying in the lab? This shows lack of motivation on your part.
  • Are you talking excessively to your friends? This goes back to the first point: should you be doing more than just talking to your friends while you’re in the lab?
  • Are you on the computer playing games or searching the Internet? These are big turn-offs for a researcher because if you’re doing this now, what will you do once you’ve been invited to join the lab? The researcher wants someone who will be a hard worker and who productive.
  • Have you read enough journal articles on the research topic that you’re not asking too basic of questions? While there’s theoretically no such thing as a stupid question, if you ask the similar questions every day, you’re being stupid.
  • Are you taking notes when you’re taught how to do a procedure in the lab? Nothing frustrates me more than if a trainer has to show you how to do something more than once. I’m not saying you have to get everything on the first round (especially if it’s a complicated technique), but you should retain some of what you learned – and the notes help you not waste the trainer’s time reviewing what you should already know.

Don’t be afraid to ask questions, lots of them! It shows that you’re interested, that you’re curious and willing to learn, and that you’re thinking about the research.

If you’re doing an experiment and it doesn’t work, think about what you did and what you might have forgotten to do. Then think about how to improve your performance of the experiment next time. Show that you’re more than a pair of hands, show that you’re actually thinking about what you’re doing in the lab.

Talk to the people working in the lab. Ask a seasoned graduate student in the lab for advice. Maybe even talk to the researcher to help you understand his expectations and how you might live up to them.

You should know that you are not the first graduate student to have a less-than-ideal experience during a lab rotation.

There’s the old saying “When life gives you lemons, make lemonade” meaning make the best of a bad situation. Keep your eyes and ears open, learn as much as you can about the research and the techniques going on in the lab. You might not stay in this lab for your graduate work, but you might be able to apply what you’ve learned to another lab rotation and deeply impress that researcher. Do the best you can with what you’re given and something unexpected and wonderful might come out of it.

If things are truly miserable and you feel you cannot finish your current rotation, you might approach another researcher about doing a mid-term lab rotation. I’ve seen a few students do this and it’s worked really well for them. Also, you can talk to your first-year adviser or graduate program director to further explore your options.

I wish you well in your endeavors!

And hopefully this advice will help you on your journey, wherever it may take you.


Debbie Knight

A Day in the Life: October 17, 2011

In research log on October 17, 2011 at 2:05 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…”

Experimental controls.

Sometimes the bane of a scientist’s life.

Without the proper controls, an experiment can look like it worked when it really didn’t. So controls are pretty important to the scientific method.

Controls can make or break the experiment. They can make a scientist yell “Eureka!” (although in my 20 years in the lab, I’ve never actually heard a scientist utter that particular word). They can make a scientist go back to the proverbial drawing board. And they can drive a scientist to find that tiny spot on the wall that says “bang head here” (a place I’ve been many times).

It’s a love-hate relationship between scientists and controls.

Case in point: my experiment last week.

I have been looking at the whether some patient populations have certain antibodies floating around in their blood. I was pretty excited that patients with susac syndrome had antibodies that bound to some very specific proteins which might help in diagnosing their disease.

So, I’d worked hard to identify those proteins.

But one piece was still missing from my story – a control of sorts.

Susac syndrome is a pretty rare disease, so most clinicians haven’t seen many cases. Because of this, some patients are initially misdiagnosed with multiple sclerosis rather than susac syndrome.

Well, it took a long (long!) ribbon of red tape, but I finally received some blood samples from multiple sclerosis patients.

And last week, I finally had the opportunity to try those specimens in my assay.

I was excited to see the results …  until I saw them.

What I expected to see: serum antibodies binding to proteins larger or smaller than the ones to which susac syndrome serum antibodies bind.

What I saw: the protein profile looked very similar to that of susac syndrome patients.

Now that’s not to say they ARE the same proteins – to determine that will require further testing.

So, this wasn’t the answer I expected. It wasn’t the definitive answer I had hoped for. But, as often happens in science, one answer to one question leads to more questions (plural).

So, while these experimental controls didn’t lead me to the answer I wanted, it lead me to an answer I needed.

I’d be a human guinea pig in a heart beat!

In observation on October 6, 2011 at 5:10 pm

Today, Reuter’s  published an article online about Dr. Ralph Steinman who died three days before he was announced the 2011 Nobel Prize in Medicine. As if winning the Nobel Prize on Monday wasn’t newsworthy enough, this scientist made himself a human guinea pig by testing several experimental therapies in his battle against pancreatic cancer. Four and a half years ago he was diagnosed with stage four pancreatic cancer which had spread to his lymph nodes. This is amazing considering a patient with such a diagnosis has about a five percent chance of surviving just one year.

I’m a big believer in medical research.

And if I had the opportunity to help advance medical discoveries like Dr. Steinman attempted to do, I would do so in a heartbeat.

That being said, I have participated several times in scientific research.

  • I’ve let researchers draw my blood more times than I can count. I even used some for my master’s project (and I have the scar to prove it).
  • I’ve donated bone marrow, allowing a researcher to drill into my pelvic bone.
  • I’ve undergone bronchial lavage — a procedure where they effectively rinse out your lung with saline so that they can collect, in this case, immune cells. I only did this once — not my best research experience.
  • I let a researcher studying stress make several blisters on my arm to monitor my ability to heal (I think I was a healthy control in this study — I wasn’t really stressed out during the experiment).
  • I’ve participated in a psychology study — took two drugs to look at how they affected cognitive ability. One kicked my brain into high gear, but for all I know it was just caffeine. The did nothing other than make me vomit. I don’t do this sort of study any more.

Being a human guinea pig by participating in research does have a few benefits.

Sometimes you get paid to participate.

For the wound healing study, I got a few hundred dollars for a weekend stay in the clinical study suite — getting paid to do my homework, watch TV, and give some blood. Not a bad deal for a college student.

And sometimes you get “useful” information.

  • One study, I found out what my tissue type was. This is the kind of information they use for organ transplantation. So in the event of a transplant, I’m set!
  • In another study, I found out that my B cells readily convert into cancerous cells in a mouse model. This information suggests it’s possible that should my immune system become compromised, through disease or old age, I’m likely to develop B cell lymphoma. Yikes! On one hand, I’m not sure I really wanted to know this. But on the other hand, it’s good to be aware (and perhaps prepared).
  • Another study has shown that I have some autoantibodies that could result in an autoimmune disease.
  • I’ve learned about some polymorphisms I have hanging out in my DNA. I’m not sure how useful this information is at the moment, but you never know with all the new discoveries being made in the molecular and cancer genetics field.

So, I totally understand why Dr. Steinman made himself a human guinea pig. If I were in a similar situation, I would as well.

And I’d try to be the best darned guinea pig ever!

A day in the life: October 5, 2011

In research log on October 5, 2011 at 2:11 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…”

My boss is working on an NIH grant proposal which is due Monday, October 17.

Plenty of time, right?

I’ve worked with three principle investigators and the story is the same – there’s always a rush to get the proposal submitted at the last minute.

You’d think we’d learn, but somehow the time gets away from us as we write and gather all the bits and pieces we need, load them into the right places on the form, and send it off by the submission deadline.

Before the electronic submission process, there were many late nights spent copying, collating, and rushing the three-inch (or more) pile of papers to FedEx at the last possible moment so it would get to the NIH on time.

Frankly, I do not miss those days!

I remember having to walk a piece of paper around for the various departmental and college administrators to sign. Now, the form just floats from one administrator to another in the digital ether – with the push of a button, each will “sign” the form electronically and pass it down the line.

I remember standing at the copier, making sure it didn’t jam as we made several copies of the proposal and all its supplemental materials. Many of those copies required additional labelling before they were completed.

I remember taping data figures into the spaces we left in the proposal.

I remember making a special trip to Kinko’s to get color copies of those pages made so that they would be included in the grant proposal. Of course, this pre-dated the office color laser printers that we would eventually use. And, of course, electronic submissions make the printing unnecessary.

Yes, I like this electronic grant proposal submission process. It certainly makes life easier. But it hasn’t eliminated the stress of submitting a proposal.  Yet.


UPDATE (October 17, 2011)

The grant proposal was officially submitted (electronically) to the NIH this morning. It seemed too easy without the last-minute copier / collating rush.

 I feel pretty good about this grant, though, in my experience, NIH grant proposals are rarely funded on the first try.  But I’m keeping my fingers and toes crossed all the same!

It takes a village…

In observation on October 1, 2011 at 12:12 pm

As Mary wanders through our lab, searching for trash bins to empty, I can’t help but think that she, along with countless other maintenance staff, is part of my research team.

She may not know how to isolate RNA or grow cells in tissue culture, but she does help the lab and its research run smoothly by carting the trash out, cleaning the floors, etc.

But Mary works almost invisibly in the background, touching not just my life, but the lives of many researchers working in the building.

Then there’s Ernie, the “light bulb guy”, who has been around since I can remember and without whom we would be working in the dark.

I used to see him pushing a utility cart filled with various sized fluorescent tubes, stopping and replacing tubes as he moved along the hallway. Nowadays, I see him carrying a clipboard, noting what fixtures need bulbs. Apparently the new and “improved” work flow has him writing down the location of fixtures and the number of bulbs that will be needed which then goes through a lengthy approval process before he can bring his cart around to actually replace the light tubes. Well, that’s “progress” for you.

Then there’s Mike, the autoclave guy, who we often call to fix the steam sterilizer that is on the fourth floor of our building.

And there’s Randy who we call when our ultralow freezers need service.

And countless others we depend on to keep things running, including maintenance personnel I’ve never seen, such as the repair dudes who somehow find a way to eek out another few months from the aging rooftop air conditioner units or the guys from “Otis” who keep the building’s elevators running safely.

Their services aren’t free. A large chunk of grant money goes toward this upkeep. If I read the financial records on my lab’s NIH grant, it looks like 52.5 percent of the grant goes toward facilities and administration costs each year.

While their jobs may not be glamorous or glorious, these people, whether they know it or not, are a part of research and I certainly appreciate their efforts.

Yes, it takes a village of people to keep research running smoothly.