microbiology
mikethemadbiologist | August 22, 2011
There's some good news and bad news regarding E. coli surveillance in meat products. The good news:
The pathogenic Shiga toxin-producing Escherichia Coli (pSTEC) serotypes known collectively as the "Big Six" will soon be banned from U.S. meat, a top expert told a meat industry conference Thursday.
Action to declare the six non-O157:H7 serotypes as adulterants in meat could come as early as next week, according to Mohammad Koohmaraie, chief executive officer for the meat division of IEH Laboratories & Consulting Group based in Lake Forest Park, WA.
For certain, he says, the Big Six --…
mikethemadbiologist | August 19, 2011In this story about the use of rapid genomic sequencing to monitor a hospital outbreak of multi-drug resistant Klebsiella pneumoniae (more details here), this end bit is interesting (italics mine):
"In the E. coli outbreak, we had enough E. coli reference strains and knew enough about E. coli biology to quickly identify a set of genes for specific diagnostics before we had the whole genome sequence," says Dag Harmsen, a microbiologist at the University of Münster who was involved in sequencing efforts during both outbreaks. "But we don't have as much experience with Klebsiella, so this time…
kcollins | July 5, 2011Born in the Eastern European province of Transylvania (known as the birthplace of Count Dracula), microbiologist Dana Perkins was raised in the former communist country of Romania and humorously describes herself as an "American by choice and vampire by birth." She chose microbiology as a field of study to understand what makes germs tick and how we can treat the diseases they cause.
Dana's love for microbiology has its roots in her childhood. "My mother was a nurse, so I spent a lot of time doing my homework in her medical office while waiting for her to finish her duties each day," says…
mikethemadbiologist | June 27, 2011Consider this a post wherein I engage in some speculation, and hope that I'm very, very wrong. You see, the 'German' E. coli O104:H4 outbreak ('HUSEC041') has taken a confusing turn:
The strain of E. coli blamed for 46 deaths in Germany appears to have resurfaced in France, the French Ministry of Health said.
The new outbreak has sickened eight people, who went to two hospitals in Bordeaux, authorities said.
Officials interviewed seven of them, all of whom reported having attended an open house at a children's recreation center. Six of them reported having eaten sprouts during the visit, "…
heathero | June 6, 2011The arsenic story continues. After much discussion in the blogosphere and elsewhere about the controversial paper claiming to have discovered life that uses arsenic rather than phosphorus in its DNA, Science has published 8 critiques of the paper and a response by the author. You can find them here. I enjoyed reading them, and was surprised at how different they all were. I am not going to dive into this because the details are summarized in Nature News, and Carl Zimmer has a great piece for Slate that also discusses the recent developments in the context of the whole story and the broader…
tsmith | June 3, 2011...when it contains a weird gene conferring methicillin resistance that many tests miss.
Methicillin-resistant Staphylococcus aureus (MRSA) has become a big issue in the past 15 years or so, as it turned up outside of its old haunts (typically hospitals and other medical facilities) and started causing infections--sometimes very serious--in people who haven't been in a hospital before. Typically MRSA is diagnosed using basic old-school microbiology techniques: growing the bacteria on an agar plate, and then testing to see what antibiotics it's resistant to. This can be done in a number of…
kbonham | May 11, 2011Maryn McKenna has a typically great post about the rise and spread of a strain of multi-antibiotic resistant Staph aureus. It arose in Holland, where it spread to pigs, picked up resistance to the antibiotic tetracycline, and then jumped back into humans. Then it spread across the EU and into the US.
As is often the case, reading McKenna's blog is fascinating, but sobering.
One of the persistent mysteries about ST398 is how far it has spread in the U.S.. That's a very difficult question to answer, because no one is consistently doing the tests that would provide data. The national meat-…
kbonham | May 9, 2011Way back in high school bio, I learned about the 2 main ways that eukaryotic organisms (everything other than bacteria and archaea) make their metabolic living: photosynthesis and oxidative phosphorylation (also known as respiration). These two processes are fundamentally related - photosynthesis combines CO2 and water to produce sugar and oxygen, while respiration breaks down sugars using oxygen, leaving water and CO2. But the cells of plants, animals and fungi can't do either of these things on their own. Sometime in our distant evolutionary past, we took on tiny passengers that do the work…
kbonham | April 21, 2011When I first got into blogging, I thought I could carve out my niche talking about the microbiome - that enormous ecosystem of trillions living inside and on every one of us. However, it's become increasingly clear that writers far more skilled than I have also decided to tackle this weighty (2-5lbs on average) subject.
Take this new paper published yesterday in Nature, describing 3 different "enterotypes" - different ways of balancing that ecosystem. I saw it last night in my Nature RSS feed, and was hoping to tackle it today.
But Ed and Carl beat me to it with a couple of stereotypically…
heathero | April 18, 2011These days it is very hip to do things eXtreme. Don't believe me? Try googling "extreme". I suppose I have jumped on the bandwagon by studying life in one of the most "extreme" environments on Earth (deep sea hydrothermal vents). The environment I study is home to the most thermally tolerant organisms on the planet, living at temperatures well above 100°C (but not boiling because of the extreme pressure). Because of my research interests, I am always on the look out for new discoveries in the realm of "extremophiles" - organisms that thrive in extreme environments. Most of them can not…
mikethemadbiologist | March 29, 2011Whenever a new discipline, especially one using a 'sexy' technology, is brought to bear on human disease, it seems to be oversold in what it will actually accomplish. In addition, every problem is suddenly viewed through that lens, that if we understand how phenomenon X influences something, then WE CAN HAZ CUREZ. I'm worried that this is happening to the human microbiome, the study of the microbes that live in and on us (Note: I'm going to call this area of study 'the human microbiome' since a term like metagenomics doesn't include classical microbiological techniques; calling it the…
neurophilosophy | March 25, 2011THE human gut contains a diverse community of bacteria which colonize the large intestine in the days following birth and vastly outnumber our own cells. These intestinal microflora constitute a virtual organ within an organ and influence many bodily functions. Among other things, they aid in the uptake and metabolism of nutrients, modulate the inflammatory response to infection, and protect the gut from other, harmful micro-organisms. A new study by researchers at McMaster University in Hamilton, Ontario now suggests that gut bacteria may also influence behaviour and cognitive processes such…
mikethemadbiologist | March 24, 2011Because we are human after all. Jason Collins at Evolving Economics, in response to my post about one economist's misunderstanding of biology, asks a very good question:
On the flip side, did Dawkins or Gould (or their respective supporters) ever concede to the other side that they were wrong and substantially change their world view?
I agree with Razib about what happened:
My own attitude is that both Richard Dawkins and Stephen Jay Gould retreated from maximalist positions when it came to the gradualism vs. punctuated equilibrium arguments of the 1970s substantively. But rhetorically they…
neurophilosophy | March 3, 2011A dead ant infected with a parasitic Cordyceps fungus (David P. Hughes).A team of entomologists working in the Brazilian rain forest has discovered four new species of parasitic Cordyceps fungi, which infect insects and manipulate the behaviour of their hosts in order to disperse their spores as widely as possible.
The modus operandi of Cordyceps is reminiscent of the famous chest-bursting scene in the movie Alien. Microscopic spores infiltrate the host via the spiracles - the holes in the exoskeleton through which insects breathe - and the fungus begins feeding on its non-vital organs.
When…
heathero | March 2, 2011Check out this explanation in the New York Times science section of the 5 second rule. For the record, this will not stop me from eating fallen food off the floor. But that's just now I roll.
heathero | February 18, 2011I got to spend last week in sunny California. I forgot how wonderful it is to sit and eat lunch outside! I was participating in a workshop held at the Department of Energy's Joint Genome Institute (JGI). The workshop was entitled Microbial Genomics and Metagenomics. Basically I spent the week learning about different tools that are available to help biologists deal with the data flood that has come out (and continues to flow faster and faster) of sequencing technologies that continue to get faster and cheaper.
Since microbes are not exactly easy to observe with ones eyes,…
mikethemadbiologist | February 10, 2011I've always thought that if Bill Gates really wanted to make his mark, he should build sewer systems in the developing world (and provide endowments to maintain them). Because I'm getting tired of reading excellent articles like this:
The recent outbreaks of cholera in Haiti, Pakistan, and Zimbabwe suggest that our current global action plans against cholera are failing. This issue contains two important articles that will help inform our discussions on ways to respond to the global cholera situation. Cholera is a severely dehydrating illness caused by Vibrio cholerae, a Gram-negative…
jtoney | February 9, 2011
Source.
Actor George Clooney is recognized for more than his roles in television and film. He has worked diligently to support human rights issues in regions in crisis such as the Sudan. In The New York Times blog "On the Ground," reporter Nicholas Kristof joins Mr. Clooney to address readers' questions about malaria.
What role do you think celebrities should play in communicating about science and medicine to the public?
While Mr. Clooney cannot offer the perspective of a researcher on malaria, or that of a scientist or physician, he can give a personal view since he contracted the…
mikethemadbiologist | January 27, 2011By way of Jonathan Eisen, we discover that museums are starting to hire microbiology curators. I'm very excited about this, probably more excited than Eisen (and he's a pretty excitable guy). In part, I've always loved museums and have thought that building microbiological collections for museums would be a neat thing to do. But there are also some vital scientific needs that would be met by museum curation.
What makes microbiological curation really exciting to me is the advent of cheap genomic methods. If you're able to culture it, we can sequence its genome, which is a pretty good way…
mikethemadbiologist | January 7, 2011Potentially, anyway. One of the challenges facing infectious disease medicine in the developing world is the cost of diagnosis: diagnostic tests are often invented in wealthy countries with access to expensive equipment and supplies (and, in those countries, these don't seem very expensive at all). Tuberculosis (TB) is difficult to diagnose in wealthy countries, and the inability to afford expensive diagnostics in the developing world--where most TB cases occur--only further compounds the problem.
So this report of a potentially cheap and more effective way to figure out if someone has…