Microbiology

i-27cf079f775070ff0ac284b81cd3a70f-10.1371_journal.pmed.0050213.g001-M.jpgI probably shouldn't find this amusing, but... Back a few years ago, a friend of mine worked at a biotech company in Seattle that had large windows looking out onto Puget Sound. They always cheered when the Navy ships came in, 'cause they knew it meant they'd ... Read more
What happens when a group of streptococci stick to cells in your throat and start to make toxins? Your body fights back by making clones. i-9752f1fb3fb5563646d156bb91c1b3b7-strep.gifThe animated video, Fighting Infection by Clonal Selection, from Etsuko Uno and Drew Berry is so good that if I didn't know better, I would ... Read more
HealthMap is a great site that could be an excellent resource when teaching a biology, microbiology, or health class. Not to mention, I can picture people using it before they travel somewhere or even just for fun. I learned about HealthMap awhile ago from Mike the Mad Biologist, but I didn't get time to play with the site until today. Here's an example to see how it works. How do I use HealthMap? ... Read more
If you like cool and unusual photos be sure to take a look at the 2008 Nikon Small World competition site. You can view lots of lovely pictures of things found under a microscope and vote for your favorite ones. You don't even have to focus the microscope! One of my favorites is the tubeworm larva. It looks something from outer space. There's even a contest to identify some of the more unconventional images. I only got three out of five. ;-( You can find them at www.nikonsmallworld.comRead more
Microbiologist develop some strange habits when it comes to food. Some take a fatalistic approach. They reason that microbes are everywhere, we're going to die anyway, we might as well eat dirt and make antibodies. You know these people. They quote things like the "10 second rule" when food drops on the floor, tell you we're all getting asthma because we're too obsessed with cleanliness, and let their dogs wash their dishes. Eeew. With a few possible exceptions, I'm in the other camp. I'm the one who freaks out if the cover is left off the salad dressing during ... Read more
Hey students: if you are looking for a summer internship in marine metagenomics and you can get your application together before June 16th, Jonathan Eisen posted information about an open position on his blog. It also looks like he's looking for post-docs (see the side bar on the right of this page.)Read more
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different ribosomal RNA genes. Many species of bacteria have multiple copies of 16S ribosomal RNA genes and the copies can differ from each other within a single genome and between genomes. Now, in one of our last projects we are determining where ... Read more
Goodbye desktop, we're off to see the web. Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve everything by using Linux. Others have ... Read more
If you're old enough or you've taken microbiology, there's a chance that sometime in your life you heard of Legionaire's disease. This disease was caused a bacteria that inhabited the air conditioners in a hotel where several veterans held a conference. Naturally, it was the microbiologists who collected samples of the bacteria and figured out what was going on. Now, there's something else going on and I'm thankful to Mike ... Read more
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to:
  1. Build a data set
  2. Align the sequences
  3. Make a tree
In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA) genes that we can find in single bacterial genomes. Bacteria contain between 2 to 13 copies of 16S rRNA genes and we' ... Read more

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