microbiology
sporte | February 26, 2008Do 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 for analysis. (this is the video below) (We split the data from one column into three).
II. Cleaning up the data…
sporte | February 26, 2008This 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. Cleaning up the data
III. Counting all the bacteria
IV. Counting the bacteria by biome
Part III. Pivot tables from Sandra Porter on…
mikethemadbiologist | February 24, 2008A while back I wrote about how the Office of Human Research Protection (OHRP) had blocked the implementation of a checklist for ICUs that would most likely prevent roughly 20,000 deaths from infectious disease annually. ScienceBlogling Revere reports that the OHRP has reversed its decision (italics mine):
The Office for Human Research Protections (OHRP) -- part of the U.S. Department of Health and Human Services -- has concluded that Michigan hospitals can continue implementing a checklist to reduce the rate of catheter-related infections in intensive care unit settings (ICUs) without…
mikethemadbiologist | February 13, 2008How antibiotic resistant your E. coli are has to do with where you've been, not what you eat.
A recent study isolated E. coli from 567 newly hospitalized patients and 100 vegetarians (one E. coli isolate per person), and screened them for resistance to X antibiotics, including ciprofloxacin, nalidixic acid, trimethoprim-sulfamethoxazole (the primary treatment for E. coli-related urinary tract infections), ceftriaxone, and ceftazidime (the last two indicate the presence of an extended-spectrum beta-lactamase, and can only be reliably treated with carbapenems).
The only significant risk factors…
sporte | February 12, 2008Well, 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:
⢠Adaptation of…
mikethemadbiologist | February 8, 2008There's quite a few infectious disease-related legislative proposals floating around Congress, so I'm going to start previewing them. I'll start with an easy one: H.R. 766, which calls for a National Infection Prevention Week (pdf here).
It's sponsored by Rep. Roger F. Wicker (R-MS) and Rep. Tim Murphy (D-PA) and has been referred to the Subcommittee on Health of the Energy and Commerce Committee in the House of Representatives (hence, the "HR"). Here's the entire text of the bill (it's short):
Whereas protecting the health of Americans includes providing every citizen with access to safe…
mikethemadbiologist | February 5, 2008I think I was a little too optimistic about MRSA (methicillin resistant Staphylococcus aureus) in pigs staying in pigs and not spreading to humans. A recent study in the Netherlands found that people exposed to pigs were 1000 times (yes, one thousand) more likely to be MRSA carriers than the general population, and the MRSA strain was usually the 'pig' strain.
What does this mean? The authors conclude:
After introduction of the new MRSA risk category in a hospital [Mad Biologist: screening those in contact with farm animals], which is located in a region with a relatively high density of…
mikethemadbiologist | January 28, 2008When I read Olivia Judson's post about hopeful monsters, I didn't think she used the term correctly (here are some good explanations why), but I was surprised by Jerry Coyne's response.
First, the personal attack on Judson is unwarranted: when we reach the point where the serious challenge to evolutionary biology is the misuse of a discredited decades-old idea, as opposed to the politically powerful anti-science creationist movement, we're in a pretty good place. She made a mistake--I don't think her motives were self-aggrandizing. Second, if you're going to launch an ad homeniem attack,…
mikethemadbiologist | January 25, 2008ScienceBlogling Tara has a great four part series examining the question of did Yersinia pestis cause the Black Death. Tara speak, you listen!
mikethemadbiologist | January 24, 2008A couple of weeks back I posted about the Office of Human Research Protections' shutting down a highly effective infection control program. In the NY Times, Jane Brody discusses the program further. Here's the list of the five things the hospitals used to combat hospital-acquired infections:
When inserting a central venous catheter, doctors should do the following:
1. Wash their hands with soap.
2. Clean the patient's skin with chlorhexidine antiseptic.
3. Put sterile drapes over the entire patient.
4. Wear a sterile mask, hat, gown and gloves.
5. Put a sterile dressing over the catheter…
mikethemadbiologist | January 22, 2008Yesterday, I posted about how feral pigs might be responsible for the spinach-associated E. coli O157:H7 outbreak. A while back, I described the epidemic spread of a new strain of MRSA throughout pigs in Europe. What was puzzling to me was why this MRSA strain, found at forty to sixty-fold greater frequency than all commensal MRSA in humans hadn't entered the human population. A recent paper in Emerging and Infectious Diseases lays out one possible reason--this strain of MRSA does not grow well on retail meat (which is thought to be a major conduit of strains from the farm to humans):
A…
mikethemadbiologist | January 22, 2008Olivia Judson describes what it would take to prevent almost all rabies deaths from Africa (rabies currently kills around 55,000 people annually):
To eliminate the disease from humans, therefore, it needs to be eliminated from dogs. And the way to do that is through dog vaccination. (At first, it may seem perverse to vaccinate dogs rather than humans, given that it's humans we want to protect. But because rabies is spread by dogs, not people, we can't break the chain of transmission unless we vaccinate the animals that spread it.)
The crucial factor in predicting the spread of an infectious…
mikethemadbiologist | January 21, 2008(Yes, it's LOLFeral Pigs)
A recent article in Emerging and Infectious Diseases just made the explanation of the E. coli spinach outbreak much more complex.
When the contaminated spinach story broke, there were a lot of accusations bandied about that this showed that either corporate factory farming was evil, or that organic farming (the farm was organic) was evil* (an aside: by now, it should be apparent to everyone that politicized public health and biological issues are often not discussed rationally or consistently). I'm no fan of corporate farming because the high densities of animals…
mikethemadbiologist | January 16, 2008The NY Times has an article about the MRSA (methicillin resistant Staphylococcus aureus) strain that is spreading rapidly among gay men. One factor is that a subset of the gay population is immunocompromised due to HIV, and consequently, is more likely to acquire MRSA skin infections.
This strain is very drug resistant, unlike most community-acquired MRSA ('CA-MRSA'). Most CA-MRSA, while resistant to methicillin, is sensitive to clindamycin. However, this strain has acquired a plasmid (a transferable 'mini-chromosome') that confer resistance to commonly-used drugs to treat MRSA:
"This…
mikethemadbiologist | January 8, 2008In most cases, assuming that the Bush Administration is up to no good and plans to do the exact opposite of what it claims to be doing is a good first principle (unless you have a "kick me" sign staple gunned to your ass). The CDC alerting passengers that they were seated near a symptomatic TB patient is not the slippery slope of tyranny, but a responsible public health response. At firedoglake, there is an idiotic post about the CDC's response to a person infected with TB on an airplane:
TB on planes: another excuse to restrict our civil liberties? You heard it here first....
This is great…
mikethemadbiologist | January 4, 2008You would think after the sound thrashing Michael Egnor received due to his mangling of the basics of evolutionary biology, the Discovery Institute might want to find someone else to quote in a guide for students. Nope:
"Microbiology tells us that bacterial populations are heterogeneous. Individual bacteria differ from one another. Molecular biology tells us that some bacteria have molecular mechanisms by which they can survive antibiotics. Molecular genetics tells us how these resistance mechanisms are passed to other bacteria and through generations of bacteria. Pharmacology helps us…
mikethemadbiologist | January 3, 2008Beta-lactam antibiotics, penicillin and all of its subsequent derivatives, are critical, life saving drugs. One way bacteria protect themselves from these antibiotics is by producing enzymes known as beta-lactamases that cleave the beta-lactam, rendering the beta-lactam antibiotic harmless. There are many different kinds of beta-lactams (such as CTX-M), and they differ in how common or rare they are.
A recent study examined looked at the role fitness might have in making TEM class beta-lactamases very frequent and found in many different species, and keeping SME class beta-lactamases rare…
mikethemadbiologist | December 27, 2007One of the lesser known microbiology facts is that the pathogen Shigella is actually E. coli. Since I'll be writing more about this cool bug soon, from the archives, here's an explanation (with a little modification).
As I mentioned in a previous post, Orac has two very good posts on MDs and creationism. In one of the posts, he links to a creationist medical student who writes the following:
Has anyone ever documented a plateful of Strep pneumo mutating into E coli? Or even into Strep pyogenes? I didn't think so. They mutate, and they exchange information. But they remain separate species…
sporte | December 24, 2007This 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.
When my husband was finishing graduate school, he brought home some agar plates that he had streaked, with different Streptomyces species, so that he could photograph them…
mikethemadbiologist | December 20, 2007From the archives comes this comment on a question raised by microbiologist Paul Orwin--"What is science?":
The only problem with Paul Orwin is that he doesn't post as often as I would like. He makes a great observation (italics mine):You've set yourself up a nice little system for examining the genome of an environmental isolate for genes involved in some important phenotype. Now, there are lots of ways to do such a thing, but lets keep it simple. You use a mutagenic technique (and there are many) to introduce random changes in the genome. You then use your powers of observation to identify…