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bacteria

Tag archives for bacteria

It’s been interesting to watch as microbiology’s own cold fusion debate has been raging. It began with an extraordinary claim about bacteria using arsenate as a replacement when phosphate concentrations are low (1).  It progressed when at least two scientist / bloggers ( here, and here) (not bloggers! the horrror! how uncivil!) gave public “journal…

The other day, one of my commenters stated that “a well-informed sixth-grader should be able to distinguish between MRSA and E. coli“. Here’s a nutrient agar plate with some of the bacteria that we isolated from a local creek last fall. We identified our bacteria by sequencing the 16S ribosomal DNA, but for various reasons,…

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…

Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we’ll answer in this last video. We’re going to use pivot tables and count all the genera that live in each biome. Then, we’ll…

This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus.

What do you do after you’ve used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What’s the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data…

For the past few years, I’ve been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to…

or E. coli, or perhaps a little Giardia (just to loosen things up, of course), or maybe even Herpes. All these scary pathogens become works of art, when Infectious Awareables puts the images on neckties. And what could be funnier than a pair of boxer shorts full of Gonorrhea?

We have lots of DNA samples from bacteria that were isolated from dirt. Now it’s time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we’re using many of the same principles.

For the record: Chlamydia is NOT a virus. I am bummed. I like the little MicrobeWorld radio broadcasts, and the video podcasts are even more fun. But I was perusing the archives and I found this: