the economic downturn hits my department

I have not yet been part of the very public, very unfortunate budget problems that have affected public institutions of higher learning... but just now, the rumors and worrying crystallized in my inbox: a proposal to hold an anonymous vote on whether to forgo the negotiated raises in our contract to help close our widening budget gap.

I'm very (very) glad to have a job, and that my university isn't laying off TT faculty. Not getting my raise, in this economic climate, isn't something I am upset about. I remember my father's salary being frozen in some years, without any cost of living increases...and those were in more flush times. So many workers in and outside of academia will make the same choice to forgo raises/have it foisted upon them. As the new fiscal year approaches... how many other academics have already decided/been told that salaries will be frozen this year? I think the universality of the problems makes losing our raises more palatable.

technically that title's true...

I was recently browsing the table of contents for the latest Applied and Environmental Microbiology, a journal that covers a very wide swath of microbiological subfields. I love reading the abstracts for interesting-sounding titles that don't necessarily pertain to my work. But I don't like it when a title lets me down. Such as:

"Interactions between Coexisting Intracellular Genomes: Mitochondrial Density and Wolbachia Infection"

Very cool idea -- both mitochondria and Wolbachia are maternally-inherited... it would make a lot of sense that they might influence one another. However, the abstract's conclusion is that they do not interact with one another. Technically, being independent of one another, not interacting, is an interaction... but it would be nice if scientists would tolerate more accurate titles reflecting negative results. But then again, I wouldn't have clicked on "Coexisting Intracellular Genomes: Mitochondria and Wolbachia do not influence each others density"... so maybe I'm part of the problem causing scientists to spin their titles in the most intriguing ways possible.

It is much more disappointing to come across a perfect-sounding title while doing a literature search, only to find out that the title, even abstract, bear little to no resemblance to what was actually done in the paper. At least we don't have to wait weeks for ILLed paper copies to get that disappointment anymore.

hot for teaching

Sometimes you just have a good lecture... the audience is listening, you're well-slept, you are getting the feedback you need to know that the class is following you. You even get questions from beyond the first row! Today, I gave a guest lecture on bacterial horizontal gene transfer, we were all collectively on, and it was an energizing experience.

It helps that I love this material -- nothing like covering conjugation, transduction and transformation for tossing in historical anecdotes, like how we first measured bacterial genomes in minutes. If that doesn't help them remember that the most commonly transferred bacterial genes due to an integrated conjugative plasmid are the ones closest to the site of integration... My asides weren't just historical, since I know a number of active researchers in the field. Amid all the talk of what good is it for large state schools to be centers of cutting-edge research, this is an example of the trickling down of research into the classroom. I was able to mention Rosie Redfield's papers, and their memorable titles (for instance, "is sex with dead cells ever better than no sex at all?"), and I was able to talk about the debate over why antibiotic resistance genes tend to be plasmid-borne, but mammalian toxin genes are usually phage-borne.

Of course, part of my excitement is because I haven't been teaching this semester, so these guest lectures are reminding me of the best aspects of lecturing -- without all the grading, emails about dead grandmothers, etc. But I'm spending the day smiling about the undergraduate student body (which doesn't always happen), and remembering that this is one of the reasons I decided against pursuing a career in industry. That, and I tried working in industry, and it was a soul-sucking experience (my PI agreed and he quit shortly after I left). But the teaching, that was part of the decision too.

anti-antibiotics

My inspirations for posts often come from what I manage to read in between deadlines and my social life, and as often as not, that means the New York Times. I don't read all the op-ed columnists... I'm in agreement with CPP about Ms. Maureen Dowd, though clearly CPP is more dedicated to reminding us that she takes up valuable column inches with her insubstantial, ill-informed populism. Which might be excusable if she were funnier, but... I read Kristof every couple of weeks, which is generally enough to keep up with his various crusades. While he's usually right, and is an articulate voice for his cause du jour, his anecdote-to-preachiness format can become stale. But lately Kristof is beating a dead horse (well, pig) that I cannot tire of: the overuse of antibiotics in livestock feed and what that means for global public health.

Here are his March 12th and March 15th columns on the topic. As a microbiologist, I tend to focus on the implications for infectious disease (the prevalence of antibiotic resistance genes in all microbes, including human pathogens), but the organ damage that comes from repeated bacterial infection that we're unable to shorten with antibiotics... another scary consequence.

I also have to give Kristof credit for the PLoS One study he cites, which comes from the lab of science blogger and awesome female microbiologist Tara Smith!

Americans' antibiotic use continues to be out of control. According to the American College of Physicians, 50% of antibiotic prescriptions each year are given to patients with viral infections, not bacterial infections. Antibiotics can help you prevent/clear up bacterial infections you have secondary to a viral infection, for instance, an ear infection that builds while one is congested with a common cold, but it cannot, will not directly clear the viral infection. Even when antibiotics are prescribed for actual bacterial infections, it irks me to no end that otherwise intelligent people do not follow the dosing instructions that come with their antibiotics. Some of my closest relatives stop their antibiotic treatments a few days early in order to have some pills to take the next time they feel an infection (possibly a viral one...) coming on. Grrrrrrr! This is wrong for so many reasons... so many reasons that I have to stop myself and maybe post about this topic another time.

But if you do have leftover antibiotics, don't flush your medicines into the water supply either... this is something I hadn't considered before finding links for this post, but flushing antibiotics also introduces those chemicals to the huge number of microbes in our wastewater and further selects for antibiotic-resistant bacteria.

As much as I could go on about all the ways that treating human infections has led to increased antibiotic resistance, including outside of developed nations with strong health infrastructures, it's something of a moot point. And that's because most of the antibiotics we use in this country are not given to humans -- they are given to healthy livestock animals. Scientific American says 70%, the UN says 50%... I think it's safe to say it's a majority of the antibiotics administered in this country every year. These drugs are not going to sick animals -- not animals suffering with bacterial infections that can and should be treated. We give antibiotics to healthy livestock because of the way we raise most of our meat in this country -- at such dense conditions, with such high bacterial loads in their environment that outbreaks of bacterial infections are inevitable.

Giving animals antibiotics also speeds their development, so our meat gets larger faster. I'm not entirely sure why this is, but I imagine that not having to spend as much energy on ones immune system would facilitate growth.

Some reading this post may know that we don't use the same antibiotics for humans and livestock. However, we effectively do. Stick a methyl group on a human antibiotic -- one that doesn't impact its antibacterial action, and it's now a livestock-ready antibiotic with the same mechanism of action... and resistances developed to livestock antibiotics show cross resistance to related human antibiotics.

I'm pretty terrified about the increased prevalence of these superbugs in communities outside of hospitals... it means the bacteria aren't at a competitive disadvantage relative to the more antibiotic-susceptible bacteria that are thought to be the majority of the bacteria in our environment. It means that humans, who carry the Staphylococcus aureus bacterium on our skins, have started carrying methicillin-resistant S. aureus as part of their normal flora. This in turn means that injuries as small as a paper cut will let those MRSA into your body...

One thing I do to reduce my antibiotic load on the environment is eating antibiotic-free meats, like the delicious local, free-range pork in a paprika sauce I ate tonight at a restaurant. I started being strict about this four or five years ago, and I definitely eat less meat than I did before. I also buy the more expensive no-hormone, no-antibiotic milk and yogurts (I can't give up my wide cheese selection though...). These small things make me feel like a more responsible microbiologist; the animal welfare improvements and the economic support of smaller farmers are secondary benefits to me. I know I'm lucky to have access to local farms that can provide these meats, and that I have the middle class income to afford them. But I think changing our agricultural policies, and what we chose to subsidize, could bring down the cost of farming that's better for public health.

challenges, indeed

I worked my way through the 52 page pdf of stimulus-package NIH challenge area grants that will be offered, and I don't think there are any calls suitable for my research. However, I did find several calls to send onto friends, and there was one hidden gem in the document:

06-RR-101* Virtual environments for multidisciplinary and translational research. Virtual networking environments like Science Commons, Facebook, and Second Life, create platforms that can eliminate many barriers in scientific collaborations. These environments integrate fragmented information sources, enable “one-click” access to research resources, and assist in re-use of scientific workflows. Funded projects would develop and implement virtual collaborative environments to facilitate biomedical and translational research, e.g. addressing issues of privacy, technology transfers, and sharing resources. Contact: Dr. Olga Brazhnik, 301-435-0758, brazhnik@mail.nih.gov

I'm not on Facebook, but I certainly understand how and why it could facilitate communication among collaborators. But Second Life??? Does it allow collaborators to work out their sexual tension virtually?? Or are there glass-and-steel biotech institutes where scientists come, wear form-fitting lab coats, prepare coffee in faux-wood alcoves near spacious conference tables and have virtual meetings?