Wednesday, January 15, 2014

Untangling the Threads of a Complex Knot

When I was a postdoc at Duke University, I spent some time volunteering at the North Carolina Museum of Natural Sciences in Raleigh. I helped visitors smush strawberries and extract DNA for the grand opening of the Nature Research Center, a new wing of the museum. In the Micro World Investigate lab, I once spent about 10 minutes staring at pond water through a microscope with an intensely focused little boy. On the stage of the Daily Planet, I gave a talk on bacterial symbionts of insects called “Bugs in Bugs” (I also had the honor of testing the AV equipment in advance of E. O. Wilson’s visit later that month). I loved my time volunteering at the museum. It is a valuable asset to North Carolina and beyond, and, even though I’ve moved away, I still consider myself a strong supporter.

It was in this context that I was surprised to read a Tweet last Saturday pointing to an announcement for a boys only summer camp at the Museum called “Science of Ick”. The announcement began “BOYS – it’s time to get icky and this camp is only for you!”. Navigating the museum’s Programs and Events page revealed that the morning slot of the first week of summer camps offered two choices for K-1 kids: a boys only “Science of Ick” and a girls only “Damsels and Dragons".

The explicit gender segregation of the camps and the language used to advertise them sparked discussion on Twitter (for a partial recap, see SciCurious’s Storify here). It’s no secret that girls and women face gender bias in STEM education and careers (for example, zero girls took the AP Computer Science Test in Mississippi and Montana in 2013). Many women who are science professionals have personally experienced bias in their K-12 education, graduate training and careers. The idea that girls would be excluded from the “icky” camp and offered only the “fairy tale” camp prompted some to recall similar instances in their own past. The ensuing Twitter conversation offered a range of valuable and balanced perspectives, including that single-sex education has benefits for girls and young women and that drawing young girls into science camp with a fairy tale theme is a reasonable strategy for increasing girls’ exposure to STEM.

Tuesday, September 17, 2013

Adding Microbial Friends to My Network - Part One

According to a recent survey, 91% of Americans own a cell phone. These phones accompany us everywhere. Cars, workplaces, malls, parks...even the bathroom. All of these places are teeming with microbial life, and our phones serve as a surface for microbial colonization. Surf the internet on the subway, take a couple photos at a pumpkin farm, or check Facebook on the toilet (...ew...), and you will likely acquire some microbial souvenirs on your phone.

Although most of these microbial hitchhikers won't cause you any harm, there are concerns about the spread of disease-causing or antibiotic-resistant bacteria on phones. For example, researchers in Scotland found 84% of hospital patients' phones were colonized by microbes, including pathogenic bacteria such as Staphylococcus aureus.

Most studies investigating microbial colonization of phones examine a single time point. But how does microbial colonization of phones proceed over time? I recently got a chance to find out! Two weeks ago, my cell phone of 6 years suffered a fatal fall (i.e., I dropped it). I dutifully reported to my local wireless store and left with a brand new smartphone. That night, I realized my old phone's misfortune was a golden opportunity for a longitudinal study of microbial colonization of mobile phones! 

With a little more foresight, I would have tromped into the store with sterile cotton swabs to sample my new phone straight out of the box. Alas, I didn't think of it until later. But I did sample my phone within 24 hours, so the results can serve as a good "baseline" for future comparisons.

The details
Awesome lab tech Lari and I used two kinds of agar plates: (1) lysogeny broth (LB) agar and (2) trypticase soy agar (TSA) with 5% sheep's blood. We used sterile cotton swabs soaked in phosphate-buffered saline to swab the front and back of the phone (in halves). We then spread the swabs over the agar and incubated the plates at 37 degrees Celsius (98.6 degrees Fahrenheit, which is internal body temperature).

The results
Here are the plates after about 36 hours of incubation.
LB agar - front of phone

Tuesday, July 30, 2013

In the Trenches: Cover Letters for Undergrads

Although the main purpose of my blog is to share fascinating microbiology, I also have interests in science education and the scientific enterprise itself. I thought about posting in a separate place on these topics, since it's a bit of inside baseball, but in the end I decided to include these posts here as a feature called "In the Trenches". Here's the first in the series, written for undergraduate students who are interested in doing research with a professor during their time in college. 

Standing out in a crowd: tips on writing cover letters for undergrads applying to lab research positions

There it is, stapled to the bulletin board in the hallway. A job announcement advertising the perfect research opportunity for you! It's a chance to work in a professor's lab, doing experiments on a fascinating topic. If you're interested in pursuing a career in science, conducting research with a faculty member during your undergraduate career is one of the best ways to develop your scientific skills and gain important experience. But, your classmates know this, too. How can you set yourself apart in a crowd of eager applicants? Write a good cover letter! Based on my experience hiring students for lab research positions, I’d like to offer a few pointers to help you craft a strong and professional cover letter for your application.

Most likely, the job announcement is a few brief sentences describing the project, a list of desired qualifications and a request to submit a resume to a particular person. Something like this... 

A work study position is available in the laboratory of Dr. Sarah Stupendous. The student will assist in studies of gene expression in bacteria exposed to antibiotics. Experience with PCR, gel electrophoresis and RNA isolation is desirable. Please submit a resume to Marcus Marvelous ( 

Some job announcements may be longer, some may even be shorter, but most share these main points: (1) what is the project, (2) what skills should you have, and (3) who to contact. In these three points lie the key to writing a strong cover letter.

Your simplest option is to open your e-mail, address a new message to Marcus Marvelous and write... 

Dear Marcus,
I am applying for the work study position in your lab. I have attached my resume.
Thank you,
Anna Aspiring 

Marcus Marvelous, a busy postdoctoral scientist in the Stupendous lab, receives this when he is waiting for an experiment to finish while eating his lunch at his desk and reading the latest, greatest research from some other lab. He thinks...<zzzzzzzzzzzzzz>.

Labs are looking for enthusiastic, self-motivated students who are eager about scientific research. Does anything in that e-mail sound enthusiastic or eager? Nope. Your e-mail should convince Marcus Marvelous that you are the perfect person for the job. Your e-mail is your cover letter, and it can make the difference between an impressive application and a boring one. In a short paragraph or two, you can do a lot to make your application stand out. Here are some tips…

Monday, June 17, 2013

Diarrhea, international politics and genome sequencing

At this time two years ago, European countries were in the grip of a severe outbreak of foodborne illness. From May to July 2011, over 4,000 people were sickened, and at least 50 people died. The culprit was a bacterium called Escherichia coli. You might find this name familiar. We have E. coli living inside us as part of our gut microbial community. These E. coli quietly exist in symbiosis with us, processing some of the food we eat and possibly protecting us from pathogens. However, some strains of E. coli are not so mild-mannered. 

The strain of E. coli responsible for the 2011 European outbreak was equipped with the genetic weaponry to cause not only gastrointestinal illness, which includes bloody diarrhea, but also a potentially fatal condition called hemolytic-uremic syndrome, which can lead to kidney failure. Investigations of this outbreak impacted international politics and deployed cutting-edge technologies, ultimately demonstrating just how much these little microbes can disrupt our carefully constructed human lives.

Electron micrograph of E. coli bacteria, magnified 10,000X.

Sunday, June 2, 2013

Return from hiatus!

It's been about two years since my last post. Yikes!

I really enjoyed working on this blog, but my research life made it difficult to find time. After two years away, I'm going to attempt to resume the blog because... (1) it was a wonderful way for me to broaden my knowledge of microbiology (unfortunately that PhD didn't come with an automatic brain download of Bergey's Manual of Systematic Bacteriology. Or maybe fortunately) and (2) it is even more important now for scientists to engage with the public. It's our job to share the wonder of science with interested listeners/readers (and the not-so-interested).

I hope to have something new posted within a couple of weeks!

Tuesday, May 24, 2011

Biofilms at 11

Every morning, millions of people voluntarily enter a place teeming with bacteria and fungi.  Despite the presence of so many microbes, we emerge from this place feeling clean and ready to start the day.  What am I talking about?  The shower, of course!

Now, it might not be all that shocking to you that your shower is a haven for microbial life.  You have probably periodically noticed mold in the folds of the shower curtain and other places.  This isn't news to you.  But the shower provides a great example to illustrate how the microbes grow.  If you have seen pictures of bacteria and fungi before, they are often portrayed as a loose collection of individual cells, typically floating around in a liquid environment.  BUT...research is proving that microbial life in nature is not that simple.  In the case of your shower, a research group led by Norman Pace (who is famous for other, non-shower-related discoveries) recently published two papers showing that an incredible diversity of microbes are growing in household showers in something called a biofilm.

As it turns out, this isn't unique to your shower.  Microbes in nature frequently grow in biofilms.  A biofilm is basically just like it is a film or mat of microbial cells held together by substances that the cells themselves secrete.  Although some biofilms are made up of only one species of microbe, many biofilms include multiple different species.  This is really fascinating, because it suggests a level of multi-cellular organization across microbial species.  Here are a couple of great micrographs of biofilms...

Wednesday, April 13, 2011

How Does It Work?: Penicillin

In the grand tradition of great sites like, I decided to start a regular feature with the terribly derivative title How Does It Work?  Why?  Well, because microbiology isn't confined to textbooks or research laboratories.  We interact with microbes every day.  We are carrying them in our guts, on our skin, inside our nose (yes, gross but true).  We eat and drink things that microbes help produce (bread and beer, for example).  Sometimes they help us and sometimes they hurt us.  So, it makes sense for us to know a little more about the different ways we study them and how we try to control them for our own purposes.

For our very first How Does It Work? today, I'll talk about the antibiotic penicillin, which was one of the first antibiotics discovered and then mass produced for treatment of bacterial infections.  Penicillin is credited with dramatically reducing the number of military deaths due to infection during World War II.  Although penicillin itself is not often prescribed these days, there are a number of antibiotics derived from penicillin that are still used in clinical therapy today, and these antibiotics work in the same general way as penicillin.

So, what is penicillin?  It is a chemical compound that is naturally produced by a fungus called Penicillium.  Below is a great picture of what Penicillium looks like under a microscope; the long filaments are called hyphae and the broom-like structures sprouting off from the hyphae are made up of columns of round spores.

Many of our antibiotics are derived from compounds produced by fungi or bacteria.  These compounds are the result of an evolutionary arms race between the different microbes that occupy the same environments.  In the case of Penicillium, this fungus lives in the soil, and it evolved to produce penicillin as a way of competing against other soil-dwelling microbes for resources.  Scientists discovered that what works for Penicillium can also work for us to combat bacterial infections.

How does penicillin work?  This may not be something you think about when you take an antibiotic.  Usually, we're just happy to take a pill and feel better.  But when you take your first course of an antibiotic, an incredible, microscopic drama starts to unfold within you.  Here's how it goes...