Microbiology

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 club" presentations on ... Read more

We had a great discussion in the comments yesterday after I published my NJ trees from some of the flu sequences. If I list all the wonderful pieces of advice that readers shared, I wouldn't have any time to do the searches, but there are a few that I want to mention before getting down to work and posting my BLAST results. Here were some of the great suggestions and pieces of advice; 1. Do a BLAST search. Right! I can't believe I didn't do that first thing, I think the ... Read more
I'm teaching an on-line bioinformatics course this semester for Austin Community College. They are in Texas of course, but I am in Seattle. This presents a few interesting challenges and some minor moments of amusement. Today, the school sent all the faculty emails telling us to stay home if we're sick. Got it. If I think I have flu, I will not fly to Texas. Instead, I'll stay home and watch videos on coughing without contaminating others. Watch "Why don't we do it in our sleeves?" and find out how you rank on the safe coughing scale. ... Read more
That's how new life forms are created every day in the wild, folks. Human researchers of course have added a few twists on the theme. If we can't induce bacteria or animal cells to collect new bits of DNA on their own, we turn to electroshock therapy. With plants.... aw heck, we just shoot them. And where did this crazy rant come from you ask? Last Saturday morning, at the crack of 9 am I got to be interviewed on a radio program with two of the main spokespeople from the DIY bio movement, Mackenzie Cowell and Meredith Patterson. The program was "The Food Chain" (you can listen to it ... Read more
Cofactor Genomics is offering to sequence a genome for a few classes for free using Next Generation DNA Sequencing technology (either Illumina GA or via AB SOLiD). Quoting from their site:
Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project could be used as an effective teaching aid in their class. We will review and choose the best entries during the month of May. Those entries will be awarded a free sequencing project ... Read more
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The 2009 Summer Research Experience for Undergraduates in Environmental Microbiology at UNLV is now accepting applications. This NSF supported program provides undergraduates with an opportunity to perform independent research under the guidance of a faculty mentor. Students will ... Read more

The other day, one of my commentors wrote that "a well-informed sixth-grader should be able to distinguish MRSA from E. coli".

Well, 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, that I won't go into here, we don't know which sequences belong to which colonies.

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. Reposted from DigitalBio's greatest hits. ... Read more
I'm sure everyone else thinks the big news today is the announcement by the Washington State Health department requiring hospitals to report MRSA cases to the state. I think the cool news is their on-line database. We'll get to that a bit later. What is MRSA? MRSA stands for methicillin-resistant Staphylococcus aureus. It's a serious pathogen that causes skin infections and greater damage if it enters the body. The Seattle Times report - a quick summary For the past three days the Seattle Times has been ... Read more
i-123d9fd0f0897dfb5be32613c5cfdb5b-mrsa_bacteria.gifHospital cases of methicillin resistant Staphylococcus aureus (MRSA) have risen 33-fold during the past ten years in Washington state, yet our hospitals fail to identify or track cases in a systemic fashion (Seattle Times). The Seattle Times began a three-part investigative report today describing the rise in MRSA ... Read more

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