Microbiology

I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found out that it was harder than they expected. Lessons learned Okay, what did we learn? 1. The community is the ... Read more
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned in assignment results with nonsensical pie graphs. So, I asked what other instructors do with software that behaves differently on different computing platforms. I never did hear from ... Read more
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA genes (It's not perfect, at least one of these genes is a ribosomal RNA methyltransferase and not a 16S ribosomal RNA.) ... Read more
Here's a fun puzzler for you to figure out. The blast graph is here:
i-02f5f2aaa95bc8ab8660ebaba090a49e-graph.png
The table with scores is here, click the table to see a bigger image: ... Read more
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 make pie graphs so that we can have a visual picture of which bacteria live in each environment. The parts of this series are: I. Downloading the data from iFinch and preparing it ... Read more
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. The parts of this series are: I. Downloading the data from iFinch and preparing it for analysis. (this is the video below) (We split the data from one column into three). II. ... Read more
Well, probably getting a stipend to help you do it. And, the really cool thing is that's part of the deal! Hustle, hustle the deadline is March 7th, and all the contact info is below. The NSF Research Experience for Undergraduates program in Environmental Microbiology at UNLV is accepting applications. This grant provides students with the opportunity to work on a research project for a 10 week period with a faculty mentor. Students receive a $4000 stipend, round trip airfare, and housing in a UNLV dormitory. Mentors have projects in the following areas: ⢠... Read more
This wasn't in the lab, but it was an accident, and it was funny later on. Normally, I wouldn't think twice about storing bacterial cultures in a refrigerator. After all, bacteria on a petri plate, inside of a plastic bag, are kind of stuck. They can't get out of the plates, and even if they did, they certainly can't crawl out of a plastic bag. I thought soil bacteria, on agar plates, were mostly harmless. I was wrong. ... Read more
or E. coli, or perhaps a little Giardia (just to loosen things up, of course), or maybe even Herpes. i-989b33e70cc1f6594d6dc025bc986fea-tie.pngAll these scary pathogens become works of art, when Infectious Awareables puts the images on neckties. And what could be funnier ... Read more
DNA sequence traces are often used in cases where:
  1. We want to identify the source of the nucleic acid.
  2. We want to detect drug-resistant variants of human immune deficiency virus.
  3. We want to know which base is located at which position, especially where we might be able to diagnose a human disease or determine the best dose of a therapeutic drug.
In the future, these assays will likely rely more on automation. Currently, (at least outside of genome centers) many of these results are assessed by human technicians in clinical research labs, or DNA testing ... Read more

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