Debbie Knight

Archive for March, 2011|Monthly archive page

Frugal times, frugal measures: An innovative model may reduce the cost of scientific research

In research issue(s) on March 27, 2011 at 7:44 am

In the university setting, a major chunk of grant money goes toward supplies and equipment needed by scientists to do research.

Traditionally, most academic research laboratories act as independent entities, even within a department. This means laboratory supplies are purchased by an individual lab, according to its own research needs. This also means that each lab is outfitted with its own equipment and instrumentation specifically used by its lab members.

This practice often leads to a redundancy of equipment within a department.

Not the best business model, I know.

Not many academic labs can afford to outfit themselves with all the equipment they might need throughout their research endeavors – especially as research needs change over time as experimental results point to new directions to explore.

It is not uncommon for a lab to use another lab’s equipment. This “sharing” of equipment resources is somewhat collaborative – though there are invisible “strings” attached, one of which is that both labs remain on good terms with each other. And nothing will destroy that working relationship more quickly than improper use of that equipment. So, the “borrowers” must tread carefully if they wish to continue “sharing” resources.

I was lucky enough to step away from tradition and participate in an innovative model for sharing lab resources.

Three years ago, I joined a research lab that was part of the Center for Microbial Interface Biology (or CMIB, for short). The central core of the CMIB was comprised of six individual labs that acted more like one large lab with six distinct research interests. During my time at the CMIB, three additional labs had been added. It should be noted that there are many more labs affiliated with the CMIB, but only the core nine labs participated in the shared resource model.

In the CMIB, all large pieces of equipment are considered communal. So, centrifuges, freezers, biosafety cabinets, thermocyclers, incubators, etc. are shared amongst all the labs – i.e., it does not belong to an individual lab.

The lab(s) responsible for equipment purchases are rotated as the needs of the community evolve. These purchases take a majority vote by the faculty members and include feedback from CMIB members, including research scientists, post-doctoral researchers, research associates, and senior graduate students. Truly, a community decision.

The advantage? This model eliminates redundancy in equipment purchases. So, one high-speed centrifuge serves nine labs instead of one.

And what about lab supplies? This model extends to lab supplies as well.

Pretty much all the labs use latex gloves, serological pipets, pipet tips, and centrifuge tubes, so these are staples maintained in a centralized storage room called the “core supply room.” And every year, in an excruciatingly long meeting, the core supply list is reevaluated, item by item. Some items remain on the list, while others are dropped or added based on the ever-changing needs of the CMIB.

A potential advantage to this system is that, in theory, the CMIB can work with vendors to reduce the cost of supplies due to the volume of supplies purchased. I say “in theory” because as far as I could tell, the CMIB has yet to successfully use its size for leveraging better pricing.

So how do the labs pay for the “core supplies’?  The metrics for calculating this is a bit cumbersome, but it goes something like this. The more personnel an individual lab has, the more money it will potentially need to kick in toward the shared supplies. But size isn’t the only parameter. It also depends on the type of personnel working in the labs.  Each class of worker is weighted in the formula. For example, a research scientist is assumed to do more research and therefore consume more supplies than a graduate student. So not only does the total number of personnel matter, but the number of research scientists, post-doctoral researchers, research associates, and graduate students working in a lab are considered when determining how much each lab contributes toward the core supplies. This is evaluated on a yearly basis.

While the advantages to sharing the cost of research supplies and equipment outweigh the disadvantages, I feel I must mention the downside of this model. For example, there is one lab in the CMIB that has such unique research needs that they pay more toward the core supplies than they actually use – i.e., this model isn’t really cost effective for them.

Another aspect of this model is the potential for waste. Here you have a room filled with supplies (envision full grocery store shelves) and unless the lab personnel are acutely aware of the cost of research supplies (and most are not), they might perceive there’s an endless supply of, well, supplies. This perceived abundance can lead to unnecessary waste, rather than using the supplies sparingly and in a cost-effective manner.

Even I, a seasoned veteran who understands how much supplies cost, had to make a mental adjustment when I left the CMIB and returned to the traditional model in February. I was amazed how I had grown accustomed to the “abundance” the CMIB offered.

Having lived in both cultures, I would wholeheartedly recommend more researchers adopt the shared resource model – especially in these times of lean federal funding.

While there are a few shortfalls that remain to be addressed, the shared resource model that the CMIB uses is a seemingly sound business principle – it reduces the overall cost of research while promoting a strong sense of community and collaboration that extend beyond the physical needs of the labs. Concepts that scientific researchers should embrace but often do not.

Please note:  all photos in this blog post were taken while I worked in the CMIB


Patient who got AIDS from a transplanted kidney: a tragedy with a silver lining?

In observation on March 18, 2011 at 12:19 pm

Human immunodeficiency virus (HIV), colour-enhanced electron microscope image, 24,000× magnification. Oliver Meckes and Gelderblom/Art Resource, New York

Can good come from tragedy? I certainly hope so.

In this morning’s newspaper, I read about the first documented case in which a patient got AIDS from a transplanted kidney.  Perhaps it might be more accurate to say that the patient contracted HIV from the transplanted tissue and because transplant patients are immunosuppressed, the HIV infection rapidly progresses to AIDS.

My first reaction to the story was dismay at the tragedy and sadness for the patient and family members. Then I got angry at the donor for not letting anyone know that there was a risk of HIV transmission. And then angry at the system for allowing this incident to happen by not testing the donor closer to the time of transplantation. And I eventually rolled over to sadness for the donor because not only does this person have to live with HIV, but he or she has to live with the knowledge that he or she passed it on to the recipient.

Then the scientist took over – the part of me that looks for what good can come of a situation such as this. I should mention that until last month I worked in a research lab that looked at how HIV is passed from mother to baby while the baby is still in the womb. I should also mention that I understood that the placental tissue samples that I used in the research came from real people with real lives, specifically mothers who were HIV-positive who may have given birth to babies infected with HIV – two tragedies with a very sobering outcome.

So, as I read the news article this morning, I realized that this unfortunate transplantation situation might be able to give researchers a unique glimpse into HIV’s lifestyle.

Okay, first I need to tell you that HIV mutates rapidly, a product of its replication machinery, and because it mutates so quickly, an infected person has many versions of the virus that differ slightly from one another due to these mutations. Some of these mutations make the virus more successful at replicating than other copies. Other mutations make the virus better at evading the host’s immune defenses. Of course, this is highly simplified, but you get the idea.

So, when someone’s infected with HIV through unprotected sex, like our donor, only one or two versions of the virus pass from the infected person to the uninfected person. The article mentioned the donor may have been infected 11 weeks prior to the kidney transplant, so that gives the HIV a chance to get a foothold and to make some mutated copies. So, when the kidney was transplanted, it probably harbored the same virus pool that was found throughout the HIV-infected donor. So the recipient had the approximately the same virus pool as the donor and the recipient was purposefully immunosuppressed to preserve the transplanted kidney.

The big question is:  what will happen to the components of the virus pools in these two individuals over time?  I suspect the viral pools would be very different – one would change more rapidly than the other, due to selection pressure exerted by the immune system.

Information such as this might help further understanding in how the virus evades as well as exploits the immune system during its life cycle. It could also help predict how the virus pools might change over time, perhaps even offer itself to computer modeling, and perhaps lead to better therapeutic strategies for HIV.

As a scientist I never wish for such a tragic situation, nor do I drool like some freakish vampire waiting for a patient with whatever disease I’m studying to pop up on the grid.

I always remember that the specimens I have in my hand are from a real person with a real disease and a real life, and my heart goes out to the patient as well as the family. This drives me to work even harder to understand the disease which might lead to a therapy or cure, so that some good can come from their sacrifice.

Fallout of the NIH Budget: Making and breaking research careers

In research issue(s) on March 17, 2011 at 10:30 am

While I’m an employee of the university, the real source of my income comes from federal funding agencies like the National Institutes of Health.

At the university we call this “soft money,” meaning my salary (and job) depend on my boss getting grant funding. So, the fate of the NIH budget ultimately affects my livelihood.  (But that’s not why I’m writing about this.)

At the moment, my boss has secured funding for two years, so I’m safe from the NIH budget woes for a short while.

However, a mid-career researcher two doors down (who I’ll call Dr. V) has his career literally hanging in the balance. If he fails to secure grant funding this time round, he will be out of the research business, which is really sad because he’s a solid and enthusiastic researcher. He studies brain cancer – and he’s on the trail of a potential new therapeutic agent that could really help patients with glioblastoma (a brain cancer with one of the worst prognosis).

The federal funding budget has been in such sorry state for the past few years, and it is increasingly more difficult for scientists to secure funding for research. And in times of lean budgets, cancer research has fared fairly well, unlike many other areas of biomedical research. However, that doesn’t mean that funding for cancer research is easy to secure, because it’s not. Case in point:  Dr. V.

Dr. V has had grant funding in the past, but he hasn’t had any for a year or so.

He submitted a grant proposal last week – and the tension is palpable. The proposal is a resubmission, which means if it doesn’t score well enough to be funded, the proposal is dead and it cannot be resubmitted for further consideration.

It may also mean his research career is dead as well.

He was once an assistant professor on the tenure track to becoming an associate professor. And now, because of his funding situation, he is no longer on the tenure track, he has no safety net if he isn’t funded, and his paycheck has been cut in half.

Normally an optimistic person, his dire situation has made him pragmatic. At this point, he says he will be relieved regardless of the outcome. If he is able to secure grant funding, he’ll be able to stay at the university and be a scientist. Life’s good. But if he doesn’t secure funding, he will find another path – one that doesn’t involve science.

This will be a loss to the scientific and academic community – he is a meticulous researcher and a great teacher (not all professors are).

Dr. V is not alone, there are many scientists in similar situations across campus and across the nation.

This has a downstream effect on future scientists.

Many graduate students see their mentors struggling with funding – established researchers as well as young researchers. Many consider alternatives to academia for their future careers, such as industry, administration, etc.

It’s just possible this will create a brain drain in the near future.

This raises concern for the future of scientific research in the United States. Federal grant funding is vital in keeping America competitive in the sciences.

I’m not sure what will happen with Dr. V, but I hope he gets his funding. It would be a shame to lose another promising researcher.



Post-script:  I found this article after publishing this blog entry which might be of  interest:  “Mid-career crunch” published in Nature.

The White Glove Test. Adventures of An Unannounced Lab Inspection

In observation on March 10, 2011 at 2:32 pm

A university radiation safety officer inspected my lab today.

And because the inspections are unannounced, there’s no way to truly be prepared for them – except to follow the safety guidelines at all times.

You would think that after all these years it would be a well-orchestrated dance and that I wouldn’t get nervous. But every inspection I get nervous – you know, awkward school girl nervous.

While I’m fairly confident that the records were maintained properly, the question “Will he find anything wrong?” always seems to pop into my head.

I guess it’s because I’m the person in charge of radiation safety for the lab. So, whether I use radioactivity or my lab mates use it, I’m the one who has to answer to the inspector should something turn up.

The inspector looks for several things, but record keeping is an area on which he will focus.

When I first started working at the university, all the record keeping was maintained on paper forms. And there were many forms – all of which had to be filled out properly.

Now, the university uses an online record keeping system which has highly simplified record keeping. However, we do still have paper records for the routine surveys we need do in the lab.

These surveys use an instrument called a “survey meter” (or a “Geiger counter”) which has a sensor that can detect certain kinds of radioactive material. We have to document those findings on a form.

The surveys also use a more sensitive technique called smear wipes which will detect all radioactive materials used in the lab. This involves taking a small piece of paper, smearing along a working surface to pick up any radioactive material that might have spilled (which hopefully it didn’t!). After the paper is placed in a container, a liquid called scintillation fluid is added — this helps enhance the signal detected by an instrument called a “scintillation counter.” Again, these findings are documented on the form.

Surveys have to be documented after each experiment.

Another thing the inspector will look for is the radioactive material we actually have in the lab – this could be the original vial the material came in or the waste generated during the experiment. All radioactive material must be accounted for.

If the discrepancies in surveys or inventory are severe enough, the lab will no longer be able to use radioactive materials. So it’s important to keep meticulous records.

It’s a lot of responsibility, being in charge of the lab’s radioactive material.  And this is why I get so nervous.

I was a little more stressed about this inspection because I had just rejoined my former lab and I had no idea what my predecessors had done or what the inspector might find. Nor did I know personally where all the radioactive material was in the lab – did they keep it in the same places as when I worked there three years ago? I certainly hoped so.

Fortunately, this inspection went well.

I was able to find all inventoried items and to show him where the paperwork was located.

So, with a big sigh of relief (until the next time) I can happily report that we passed the inspection with flying colors.