microbiology
mikethemadbiologist | December 20, 2007By way of Amanda, I came across this NY Times op-ed by Michael Pollan that discusses the role of agribusiness' misuse of antibiotics in the rise community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA). I've talked about the MRSA 'pig epidemic' before, and, Intelligent Designer knows I've talked about the misuse of antibiotics in agriculture, such as the attempt to get cefquinome approved for use in agriculture (Sack, met Mr. Stupid and Ms. Hammers). But I'm not sure that Pollan is correct about this.
The strain of CA-MRSA found in pigs is nothing like those found in healthy…
mikethemadbiologist | December 19, 2007
...the Chikungunya virus might have something to say about that (if it could speak). From PLoS Pathogens:
Chikungunya virus (CHIKV) is an emerging arbovirus associated with several recent large-scale epidemics of arthritic disease, including one on Reunion island, where there were approximately 266,000 cases (34% of the total island population). CHIKV is transmitted by Aedes species mosquitoes, primarily Ae. aegypti. However, the 2005-2006 CHIKV epidemic on Reunion island was unusual because the vector responsible for transmission between humans was apparently the Asian tiger mosquito, Ae.…
mikethemadbiologist | December 13, 2007If you visit ScienceBlogs regularly, you've probably read about ScienceBloglings Sheril Kirshenbaum's and Chris Mooney's proposal for a presidential debate about science. There's a lot I like about this proposal, but the reality of what could happen bothers me. First, what I like about the idea.
For much of the last two and half years, I worked at a non-profit organization that focused on infectious disease policy and programs. Science policy--and politics--are important. The idea that every political candidate would actually have to devise a science policy, and perhaps even be judged by…
mikethemadbiologist | December 12, 2007Earlier this week, I attended the International Human Microbiome Consortium Meeting (the human microbiome consists of the organisms that live on and in us). I'm not sure to make of the whole microbiome initiative, but one thing is clear to me: this is being driven by the wrong group of scientists.
Instead of being directed by biologists (medical primarily) who have devised a set of important questions, and want to use the power of high throughput genomics, including metagenomics which sequences of all the DNA in a specimen--bacteria, viruses, fungi, protozoa, and, yes, human (which raises…
sporte | December 6, 2007or 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?
mikethemadbiologist | November 30, 2007Or is it Lazarai? Either way, The New Yorker has an interesting article about recreating extinct viruses. To be precise, the article deals with recreating retroviruses.
Before you get all het up about the Evul Scientists creating a new AIDS or some hooey, most mammalian genomes (and other organisms) are chock full off degenerate--non-functional--retroviruses. Presumably they would up in these genomes by infecting the host, so figuring out what ancient viruses look like can help us figure out how today's viral threats work. While there's some hyperbole in the article, it's still a pretty…
sporte | November 15, 2007DNA sequence traces are often used in cases where:
We want to identify the source of the nucleic acid.
We want to detect drug-resistant variants of human immune deficiency virus.
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 companies, who review these data by…
mikethemadbiologist | November 8, 2007
The Charge of the Light MRSA Brigade
A few months ago, I discussed an article that demonstrated that pigs had ridiculously high frequencies of MRSA. ScienceBlogling Revere discusses another paper about pigs and MRSA. Like the previous study (published by some of the same authors), several of the same conclusions can be drawn:
These are astronomical rates of MRSA, relative to anything outside of a clinical setting--and the Netherlands' MRSA frequency is an order of magnitude lower than the U.S.
One piece of evidence argues for the hypothesis that the use of antibiotics in agriculture,…
mikethemadbiologist | November 5, 2007If don't already know, the world's frog (and other amphibian) populations are facing a massive decline. One cause is an infection by chytridiomycosis, a fungal disease. Scientists in New Zealand have announced that treatment with chloramphenicol, an antibacterial agent can cure chytridiomycosis:
Fearful that chytridiomycosis might wipe out New Zealand's critically endangered Archey's frog (Leiopelma archeyi), the researchers have been hunting for a compound that would kill off the disease's trigger, the fungus Batrachochytrium dendrobatidis.
They tested the chloramphenicol candidate on two…
sporte | October 31, 2007When purified, it glows with an unearthly light. You can't go "chemical free" and try to escape it. It's part of our bones and it forms the backbone of our DNA. A tool for good, a tool of war, essential for gardening, and infamous as a pesticide; phosphorus is truly an amazing element. Amazing too, are the stories about it's discovery and our history with using it. Many of the stories in The 13th Element by John Emsley (2000, John Wiley & Sons), from the alchemist's bench to the murderer's kitchen, are well-suited to reading on a Halloween eve.
From the nightmare inspiring stories…
mikethemadbiologist | October 31, 2007I have a week off, so I've been going to the gym in the morning later than usual. I'm still recovering from the near-lobotomization of morning radio, so I wasn't prepared for a report on the "superbug" on Fox's The Morning Show with Mike and Juliet--think of it as a cheap knockoff of Regis and Kelly. Since the sound wasn't turned on for the television, I should have just left it alone, but no, I had to check out the video on the interwubs when I came home.
First, anyone who says that evolutionary biologists suck at communicating should watch this bozo. It's a classic example of how not to…
sporte | October 28, 2007Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome.
Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out who else shares our bodies, and lives in our skin, in our stomachs, and other places where the sun doesn't shine. Craig Venter used metagenomics when he sailed around the world and sequenced DNA samples from the Sargasso Seas.
In this…
sporte | October 27, 2007The simple fact is this: some DNA sequences are more believable than others.
The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad."
All they see are the base calls and sequences: ATAGATAGACGAGTAG, without any supporting information to help them evaluate if the sequence is correct. If DNA sequencing and personalized genetic testing are to become commonplace, the practice of ignoring data quality is (in my opinion) simply unacceptable.
So, for awhile anyway, I'm making a…
sporte | October 26, 2007We 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.
The general process is this:
1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is good, and measure how good it is, but it cannot turn bad data into good data. And, there's no point in wasting time with…
sporte | October 25, 2007The next time you bite into a crisp juicy apple and the tart juices spill out around your tongue, remember the honeybee. Our fall harvest depends heavily on honeybees carrying pollen from plant to plant. Luscious fruits and vegetables wouldn't grace our table, were it not for the honeybees and other pollinators.
Lately though, the buzz about our furry little helpers hasn't been good. Honeybees have been dying, victims of a new disease called "colony collapse disorder," with the US, alone losing a large number of hives in recent years.
Why?
Researchers have speculated about everything…
mikethemadbiologist | October 25, 2007
Yes, it's LOLStaphylococcus. They don't call me the Mad Biologist for nuthin'
A colleague of mind sent along this paper, "Nose Picking and Nasal Carriage of Staphylococcus aureus":
OBJECTIVE. Nasal carriage of Staphylococcus aureus is an important risk factor for S. aureus infection and a reservoir for methicillin-resistant S. aureus [MRSA]. We investigated whether nose picking was among the determinants of S. aureus nasal carriage.
SETTING AND PARTICIPANTS. The study cohort comprised 238 patients who visited the ear, nose, and throat (ENT) disease outpatient clinic of a tertiary…
sporte | October 24, 2007Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?
This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman. (See see "Sequencing the campus at the Johns Hopkins University" for more background.)
We are going to do a bit of metagenomics by using FinchTV and blastn to identify the soil bacteria that were sampled from different biomes and then use an SQL query that I…
mikethemadbiologist | October 23, 2007Because this week is really hectic, I just want to follow up on this post I wrote about MRSA.
One of the hidden stories in the rise in the frequency of antibiotic resistant bacterial strains is that this has also been accompanied by an absolute increase in the number of infections. In other words, it's not the case that you used to have 90 sensitive infections and 10 resistant infections per year in your hospital, and now, you have 50 sensitive and 50 resistant infections (which would be bad enough). Instead, you have the same 90 sensitive infections and 90 resistant infections (for a…
mikethemadbiologist | October 17, 2007According to the Boston Globe, a new study indicates that deaths from the bacterium Staphylococcus aureus ('staph infections') have exceeded AIDS/HIV deaths in the U.S (italics mine):
Deaths tied to these infections may exceed those caused by AIDS, said one public health expert commenting on the new study. The report shows just how far one form of the staph germ has spread beyond its traditional hospital setting.
The overall incidence rate was about 32 invasive infections per 100,000 people. That's an "astounding" figure, said an editorial in Wednesday's Journal of the American Medical…
mikethemadbiologist | October 2, 2007One of the major fallacies of intelligent design creationism is that so many structures appear to be haphazardly designed. Case in point: polyadenylation in Giardia lamblia. ScienceBlogling Carl Zimmer, in an excellent post about the recently published Giardia genome, describes the system:
There's all sorts of fascinating stuff lurking in Giardia's genome. As they surveyed its 6470 genes, the genome team was struck by how simple Giardia is, compared to other eukaryotes. I think this diagram in particular does a nice job of illustrating Giardia's simplicity. The top drawing shows what…