My Delight, but a Germophobes Nightmare

I am always (perhaps too much) scanning the blogosphere for anything related to FredCoBio news.  This story I predict will make the Network news tonight or maybe tomorrow.

The entire article is published in Science (and will require a paid subscription to view your tax dollars at work), but ther have been a number of AP stories circulating on the blogesphere today. You can read the whole story at ScienceNOW:

Your Body Is a Wonderland … of Bacteria

By Stephanie Pappas
ScienceNOW Daily News
28 May 2009

Where can you find your skin’s most diverse community of bacteria? Not in a sweaty armpit or linty belly button. According to a new survey of the bacterial ecosystem that covers us, the diversity hot spot of the body’s exterior is the forearm. And the surprises don’t end there.

Microbes that live in and on our bodies outnumber our own cells 10 to one, but researchers have only recently begun to catalog the residents on our skin. Traditionally, scientists identified human skin bacteria by swabbing volunteers and culturing the samples, but those results skewed toward microbes that grow well in the lab. Thanks to ever-evolving gene-sequencing technology, scientists can now use microbial RNA to identify organisms. With these techniques, researchers have found an unexpectedly wide variety of bacteria on human skin (Science, 23 May 2008, p. 1001). But no one had ever systematically compared bacterial colonies from different areas on the human body.

To do so, scientists from the National Human Genome Research Institute in Bethesda, Maryland, recruited 10 volunteers and asked them to wash with mild soap for 1 week. Then, after 24 hours without bathing, the volunteers arrived at the lab, where researchers swabbed and scraped their skin in 20 places–everywhere from the nostril to the navel to that bane of low-rise jeans aficionados, the gluteal crease. The team analyzed ribosomal RNA from the samples and classified the microbes based on their genomes.

The researchers found about 1000 species total, which were fairly consistent from person to person; it turns out we all have similar tenants in our noses and on our backs. The number suggests that our skin is as variegated as our guts, which house anywhere from 500 to 1000 bacterial species. The team also found vast differences across the skin, according to the study published in tomorrow’s issue of Science. Contrary to what acne-prone teenagers might expect, oily areas such as the forehead and scalp are actually less diverse than dry areas such as the forearm (though one is enough for grief: Propionibacterium acnes thrives in oily spots). The most barren region was behind the ear, with a median diversity of 15 species. In comparison, the forearm teemed with a median 44 species. A follow-up with five of the volunteers months later found that bacterial makeup changed little over time.

The link to FredCoBio is simple. Alice Y. and I worked together in at Molecular Diagnostic Division of Life Tech, which is now known as Digene/Qiagen.  She used to give us so many clothes passed down from her daughter, Rachel, to our oldest (now 20, yikes!).  And Bob B. is an original BRL guy who lives in Frederick.  I remember his wife worked the cash register at Martins on 7th street when we used to live in the city.  Anyway, they are both at NHGRI now, along with a number of other former Life Tech people.

Pretty cool research and yet another deep tie into the FredCoBio community.

Mushroom hunting: Let the Festivities begin!

At SciFoo at Google in August ’08 I met Paul Stamets of Fungi.com.  One of the many give a ways was his book, Mycelium Running.  I have been obsessed ever since.  I had the opportunity to ask Paul about cultivating morels I have my yard.  I am watching and waiting for my morels to sprout (which is typically 2-5 days after the first heavy rain in April in this region), but in the mean time I am checking out what’s come to fruit after the rains this weekend.  I’ve also propagated some shiitake (which I bought at fungi.com in the form of plug spawn) and some shaggy parasol mushrooms I picked out of the goat yard in the fall.  I am cultivating these in corrugated cardboard (in one case a pizza box) which I left out over the winter.  The mycelium are running, but I am worried I have some undesirable mold running, too.  Time will tell.

In any event, I put together this enjoyable slide show of my Sunday morning mushroom adventure (updated with music):

Now that I have moved my operations into FITCI@Hood, I hope to take advantage of the Hood Biology department to help me identify some of these fungi.  I bought the National Audobon Societies Field Guide, but I can never make a firm identification.  you don’t want to be making bad taxonomic decisions when it comes to wild mushrooms.  Any experts ut there who would like to start a c”shroom hunting Club?  One interesting thing about Paul is that he was the Ken Kesey & the Merry Prankster’sofficial mycologist.

I think I have blogged his TED talk before, but it’s worth another post

City Steps up Bioremediation of Algae in Carroll Creek

We have all waited with great anticipation for the development of the Carroll Creek Promenade through downtown. As many of you know, seasonal flooding of Carroll Creek has prevented development of the of area historically. Back in the late 70′s, after flooding of a good portion of downtown following hurricane Agnes in 1972, the idea of a flood control project (with associated retail development) was born. The past few years have seen the project come to fruition, with new Condos popping up and restaurants like La Paz, the Green Turtle and Hinode all drawing attention.

One problem became obvious in the middle of last summer season: the flow in the creek was so slow that algae soon overtook the scenic waterway, rendering it a sludgy, slimy, smelly green cesspool. A process we biologists refer to as eutrophication. This is a bit of a misnomer and has always fascinated me with respect to etymology. From the Greek eutrophos, well-nourished : eu-, meaning “good” and trephein, to nourish. But from a practical stand point, this really comes to mean making waters rich in mineral and organic nutrients that promote a proliferation of plant life, especially algae, which reduces the dissolved oxygen content and often causes the extinction of other organisms.

I was interested to read in the Gazette yesterday that the City has contracted a firm, Bioverse, of Minnesota, to take action against our beloved slime. They will install a number of AquaSpherePRO devices, which are spheres of beneficial bacteria and enzymes: a Probiotic prescription, of sorts.

We hope that the combination of the Bioremediation and improved water flow (which increases to dissolved oxygen and inhibits algae formation) will work and we can walk along the creek this summer unencumbered by the stench that is biology.

Genome Projector

I ran across this neat little tool called the Genome Projector via My BioTech Life. It’s a Google Maps based graphics program which contains 320 bacterial genomes and gives you a zoomable view of circular DNA sequences, pathways and a DNA walk. It’s pretty cool and I’ll link it in the Gene Jockey section later. Why don’t you give it a try?