microbiology
mikethemadbiologist | September 2, 2008A recent, must-read article for anyone concerned about the problem of misuse of antibiotics to treat viral bronchitis, not to mention anyone who prescribes antibiotics, was recently published in Clinical Infectious Diseases. The short version: giving patients antibiotics to treat viral pneumonia is dangerous for the patients themselves (never mind the evolutionary consequences of increasing resistance).
Since antibiotics are almost never effective against bronchitis, the prescribing rate should be nearly zero, but in the U.S., 67% of adults with acute bronchitis received antibiotic therapy…
mikethemadbiologist | August 18, 2008
This is not good. A recent article in Emerging Infectious Diseases describes two separate cases of community-acquired ST398 MRSA--and neither case was associated with agriculture. Let me explain what this means and why this is really bad news.
MRSA--methicillin resistant Staphylococcus aureus--is a serious problem: in the U.S., it kills more people annually than AIDS. Typically, the therapy used to treat MRSA is vancomycin, and strains resistant to vancomycin can't be treated on-label with any commercial antibiotics*. ST398 is a new clone of MRSA that is thought to be associated with…
mikethemadbiologist | August 17, 2008In a very interesting NY Times magazine article about wastewater treatment (no, really, it is worth reading), I came across this passage:
http://www.nytimes.com/2008/08/10/magazine/10wastewater-t.html?_r=1&ref…
And then there are those whose first, and final, reaction is "yuck."
"Why the hell do we have to drink our own sewage?" asks Muriel Watson, a retired schoolteacher who sat on a California water-reuse task force and founded the Revolting Grandmas to fight potable reuse. She toured the Orange County plant but came away unsatisfied. "It's not the sun and the sky and a roaring river…
mikethemadbiologist | August 11, 2008I realize science is hard and stuff, but there are serious problems with the evidence in the anthrax investigation. I'm not the only who thinks so: ScienceBloglings Tara and Revere think so too, along with most of the commentors. Thankfully, these problems are finally starting to enter the discussion. First, from Glenn Greenwald:
The NYT today has an excellent Op-Ed from a microbiologist (the former Chief of Fort Detrick's bacteriology division) pointing out the numerous deficiencies in the FBI's scientific assertions. Critically, that Op-Ed describes the properties of the high-grade…
mikethemadbiologist | August 7, 2008Yesterday, I mentioned my doubts about there being two anthrax strains used in the 2001 attacks. Thanks to an article identified by reader TomJoe, I'm convinced that there was only one anthrax strain involved, if the only evidence for the existence of two strains is that there is a DNA inversion.
Just to remind everyone, this is what I mean by a DNA inversion:
In many bacteria, inversions are used as regulatory mechanisms--when the DNA is in one direction, nearby genes are turned on, and when in the other, they're turned off. Like so (this is a made up example for illustrative purposes only…
grrlscientist | August 6, 2008tags: virology, mimivirus, sputnik, virophage, microbiology, molecular biology
Now here's an astonishing discovery that's hot off the presses: a virus that infects other viruses! This amazing finding is being published tomorrow in the top-tier peer-reviewed journal, Nature.
I don't know about you, but when I was in school, I was taught that viruses could only infect other living cells, and further, I was taught that viruses are not living cells. So, logically, one could conclude that viruses cannot infect other viruses. But a new discovery by a group of scientists in France reveals…
mikethemadbiologist | August 6, 2008In reading this NY Times story about the anthrax investigation, this statement about how the presence of an inversion (a region of flipped DNA) puzzled me (italics mine):
The genome of various stocks of the Ames strain of anthrax used in the attacks were almost identical in all the 5 million chemical letters of their DNA. But researchers found enough differences in the attack strain to provide a reasonable chance of identifying its source.
The chief difference was that a stretch of DNA was flipped head to tail in some bacteria in the attack strain, but not in any other samples.
Further, the…
sporte | August 6, 2008Microbiologist develop some strange habits when it comes to food.
Some take a fatalistic approach. They reason that microbes are everywhere, we're going to die anyway, we might as well eat dirt and make antibodies. You know these people. They quote things like the "10 second rule" when food drops on the floor, tell you we're all getting asthma because we're too obsessed with cleanliness, and let their dogs wash their dishes.
Eeew.
With a few possible exceptions, I'm in the other camp.
I'm the one who freaks out if the cover is left off the salad dressing during dinner. I brush my…
grrlscientist | August 4, 2008tags: researchblogging.org, Macaw Wasting Disease, myenteric ganglioneuritis, proventricular dilatation disease, Bornaviridae, avian bornavirus, negative strand RNA viruses, pan-viral microarray, ViroChip
One pair of the Little Blue (Spix's) Macaw, Cyanopsitta spixii.
This species is extinct in the wild and its captive population consists of roughly 70 to 100 individuals.
Image: Fundação Parque Zoológico de São Paulo (São Paulo Zoo), Brasil.
For more than 30 years, a mysterious disease, known as proventricular dilatation disease (PDD), has sent chills of terror down the spines of…
mikethemadbiologist | August 3, 2008Glenn Greenwald's recent post about the botched anthrax investigation reminds me of a colleague who was investigated by the FBI after the anthrax attacks (and check out the letter claiming that Bruce Ivins was yet another scientist wrongfully accused).
When I heard that he was under investigation, I was shocked: he is one of the nicer scientists I know. Ultimately, he was cleared, and in a bizarre reversal, the government asked him for help in typing the anthrax strain.
The reason I bring this up is not to demonstrate that the FBI couldn't investigate its way out of a paper bag, but to note…
mikethemadbiologist | July 30, 2008
With all of the stories about bacterial contamination of food, a recent paper describes one possible way to reduce the virulence--the ability to cause disease--of the bacterium Escherichia coli.
Farms are an obvious...input of E. coli--the amount of feces that a single pig produces is staggering, never mind a thousand pigs*. The concern is that E. coli from agricultural settings can either serve as a genetic reservoir of virulence (disease-causing) genes (and antibiotic resistance genes too), or as a source of virulent E. coli strains, such as E. coli O157:H7.
What the authors of paper…
grrlscientist | July 30, 2008tags: researchblogging.org, dinosaurian soft tissue, fossils, bacterial biofilms, paleontology, endocasts, formerly pyritic framboids, collagen
Figure 1. EDS spectrum of framboid. EDS spectrum of framboid showing an iron-oxygen signature. Pt is from coating for SEM. Area in red box was scanned for elements. [larger view].
DOI: 10.1371/journal.pone.0002808.
Some of you might remember a paper published in Science that rocked the paleontological world by revealing that a broken thigh bone from Tyrannosaurus rex contained soft tissue. When this soft tissue was analyzed, it was identified as…
sa smith | July 28, 2008Astute ERV readers have noticed a couple of odd things about my research.
1- How the hell am I cutting and pasting bits of a retroviral (RNA) genome together?
2- How the hell do I have a (seemingly) endless supply of HIV-1 for my experiments?
The answer to both questions is, infectious molecular clones!
Short explanation-- Infectious molecular clones are just viral genomes (as DNA) inserted into plasmids. Even though plasmids are only found in bacteria (our cells have no idea what to do with the things), you can then use some chemistry tricks to get a mammalian cell line to read the plasmid…
grrlscientist | July 27, 2008tags: researchblogging.org, Bombus impatiens, Bumblebees, pathogen spillover, epidemiology, pollinating insects, greenhouses
Common Eastern Bumblebee, Bombus impatiens.
This species is often relied upon to pollinate commercial food crops,
such as tomatoes, that are often grown in agricultural greenhouses.
Image: Wikipedia Commons [larger view].
A mysterious decline in North American bumblebee populations is apparently the result of "spillover" of pathogen-infected commercial bumblebees, Bombus species, from agricultural greenhouses where tomatoes, peppers and cucumbers are commonly grown…
mikethemadbiologist | July 25, 2008I've written before about antibiotic resistance in the developing world. Because these poor communities don't have access to many antibiotics, one wouldn't expect high frequencies of resistance to antibiotics. Resistance to ciprofloxacin ('Cipro') is all the more shocking because these communities don't have access to this relatively expensive drug*. Not only is ciprofloxacin resistance observed, but, in these communities, it occurs at higher frequencies than in intensive care units in developed countries.
So what's a possible culprit?
Sadly, a recent paper in PLoS ONE suggests that…
sa smith | July 21, 2008Bless their hearts. The Creationists over at Answers in Genesis are working their perfectly designed fingers to the bone. Blowing the Discovery Institute out of the water by not only publishing a for-realsies science journal (well, at least once), but also performing 'semi-technical' research!
Darwin at the Drugstore? Testing the Biological Fitness of Antibiotic Resistant Bacteria
While its just adorable to see them working so hard, their crippled understanding of basic science leaves this semi-technical article completely worthless.
Problem #1-- Comparing Chihuahuas to Great Danes
If *I*…
grrlscientist | July 18, 2008tags: Microcosm, microbiology, bacteria, E coli, evolution, Carl Zimmer, book review
I lived through Seattle's outbreak of the "killer E. coli strain O157:H7" that charged into the world's consciousness after it mercilessly destroyed the kidneys and other vital organs of hundreds of children and adults who consumed contaminated fast food. During this time, I worked as a lab microbiologist in several human and veterinary hospitals in the Seattle area while I earned my bachelor's degree in microbiology, so I have a strong background in both the practical realities and the scientific lore of…
mikethemadbiologist | July 14, 2008...seven years later? The bad news--for years, cephalosporin antibiotics (antibiotics derived from penicillin, such as ceftiofur, cephalothalin, cefoxitin, and ceftriaxone) were used 'off-label' (meaning irresponsibly) in agriculture (italics mine):
Inspectors found a common antibiotic has been misused in animals through practices such as injections into chicken eggs and ordered farmers to stop the unapproved treatments because of the risk to humans.
The drugs, called cephalosporins, were given in unapproved doses to chickens, beef, pigs and dairy cows, the U.S. Food and Drug Administration…
mikethemadbiologist | July 11, 2008One of the things I find fascinating about the Weather Channel is that after watching it for a while, you actually start to worry about that cold front moving through some other part of the country. You become quite paranoid about things that won't affect you. Well, I've got an even better way to drive yourself nuts about scary things that won't affect you: HealthMap.org.
I'm kidding. Healthmap.org is actually really interesting--it gives you a visual representation of all of the disease outbreaks globally. You can change the dates, diseases, and locations you want to look at. It also…
mikethemadbiologist | June 26, 2008In a Journal of Infectious Diseases commentary about this article, there's a fascinating discussion of the relationship between the HTLV-1 virus, which can cause T-cell leukemia in about one percent of those infected, and gastric cancer caused by the bacterium Helicobacter pylori. And it's not what you would expect.
Here's the summary (italics mine; references removed for clarity):
In this issue of the Journal, Matsumoto et al. asked whether human T lymphotropic virus type 1 (HTLV-1) antibody status is associated with the risk of developing gastric cancer. In a cohort of >5000 patients…