microbiology
grrlscientist | October 16, 2009tags: Lab Trash, recycle, molecular biology, cell biology, streaming video
I've been telling you about the perils of plastics, but some of the worst plastics offenders are molecular and cell biologists. Nearly every experiment that we do uses incredible amounts of plastics. In cell biology or molecular biology labs the emphasis is on working sterile, quickly and reproducibly. So companies have been selling all these incredibly useful products to life science labs: sterile plastic tubes of all shapes and sizes, single wrap multi-well tissue culture plates, sterile plastic dishes, sterile…
terrasig | October 7, 2009Welcome visitors coming from a recommendation by Dr Carmen Drahl at C&ENtral Science, the blog of the American Chemical Society's Chemical & Engineering News (C&EN):
Terra Sig has a fantastic post about the chemistry prize. The money quote: "If I see electrons being pushed around, it's chemistry."
Thank you for the kind words, Dr Drahl. New readers, feel free to weigh in down in the comments as to your take on this year's Chemistry prize.
The 2009 Nobel Prize in Chemistry has been awarded to three amazing scientists who elucidated the chemical bond-by-chemical bond action of the…
mikethemadbiologist | September 30, 2009One of the thing we need to pay attention to during TEH SWINEY FLOO! is the role of bacterial infections in flu-related mortality: a fair number of the deaths ultimately could result from a secondary bacterial infection by organisms like Staphylococcus (including MRSA), Streptococcus, and some of the Gram-negative organisms. Unfortunately, this is happening in a significant fraction of cases:
Nevertheless, the 22 cases (among 77 deaths confirmed to be from H1N1) emphasize that bacterial co-infections are playing a role in the ongoing pandemic, something that was not clear at first, the CDC…
sa smith | August 25, 2009Okay, no big shock to any of you-- bacteria are becoming resistant to our antibiotics. One of the many enteric bacteria (cause kids to poop to death), E. coli, is racking up antibiotic resistance genes like theyre McDonalds Beanie Babies.
What the hell are we going to do?
Phage therapy.
Bacteriophage are viruses that eat bacteria... lol... Bring in the gators to eat the snakes.
For a long time it was ignored as an option in the US (eh, Soviet medicine). It doesnt help that the Soviet 'science' behind phage therapy is murky-- yeah, they have commercially available phage therapies, but…
mikethemadbiologist | August 12, 2009In the midst of the concern about TEH SWINEY FLOO!, very few people (other than the Mad Biologist), have been discussing the double whammy of influenza followed by bacterial infections. A couple of years ago, I first started describing reports of KPCs:
No, KPC isn't a new fast food restaurant. It's short for Klebsiella pneumoniae carbapenemase. The bad news: it's very hard to treat. The good news: it's very rare...for now.
Actually, the correct term is KPC-possessing K. pneumoniae [these genes are now showing up in other bacteria], but we'll just use the slang 'KPC'--it's what all the cool…
mikethemadbiologist | August 6, 2009...assembly and analysis. The Wellcome Trust has a very good (and mostly accurate) article about the 'next-gen' sequencing technologies. I'm going to focus on bacterial genomics because humans are boring (seriously, compared to two bacteria in the same species, once you've seen one human genome, you've seen them all).
Most of the time, when you read articles about sequencing, they focus on the actual production of raw sequence data (i.e., 'reads'). But that's not the rate-limiting step. That is, we have now reached the point where working with the data we generate is far more time-…
grrlscientist | August 5, 2009tags: potable water, safe drinking water, LifeSaver Bottle, streaming video
Too much of the world lacks access to clean drinking water. In this video, engineer Michael Pritchard did something about it -- inventing the portable Lifesaver filter, which can make the most revolting water drinkable in seconds. An amazing demo from TEDGlobal 2009. [10:05]
TEDTalks is a daily video podcast of the best talks and performances from the TED Conference, where the world's leading thinkers and doers give the talk of their lives in 18 minutes.
mikethemadbiologist | July 15, 2009In light of the policy mediocrity that is the Obama administration, it's refreshing to read that the Obama administration is supporting the Preservation of Antibiotics for Medical Treatment Act (PAMTA). Of course, it's early days yet, so it would be par for the courseis quite possible that Obama's support for this legislation will crumble.
I've discussed the bill in greater detail elsewhere, but here's why this bill would greatly improve our antibiotic use policy:
It covers all classes of antibiotics; there are no exempt classes of drugs.
The definition of "non-therapeutic use" is very…
mikethemadbiologist | July 13, 2009Sometimes, it's not the high end technology that saves lives, but the cheaper low end stuff. One of the ways microbiologists identify different bacteria is by growing them on 'defined' growth media. We have built up a vast knowledge of which growth conditions will support particular bacteria (and what those bacteria will look like on those media).
One of those media is blood agar plates.
A biological sample, such as infected blood, sputum (the gross stuff you hack up), or other disgusting bodily fluid will be cultured on an agar plate that contains a variety of nutrients (the agar, derived…
sa smith | July 10, 2009RU-486, or mifepristone, was approved for use in 2000 in the US, for medical abortions.
Shortly there after, something weird started happening. A handful of women who used RU-486 were dying from sepsis, caused by a really rare bacteria, Clostridium sordellii. Like, these women didnt have AIDS. They werent meth addicts or recovering from cancer. They were previously completely healthy 18, 22 year-old women dropping dead.
To pro-lifers, the message was clear: Abortion kills women.
Planned Parenthood's recommendation to use the abortion-causing drug Misoprostol vaginally rather than orally…
mikethemadbiologist | June 10, 2009
I've been meaning to get to a really interesting article titled "Killing niche competitors by remote-control bacteriophage induction." So, let's talk about your nose.
Two species that are found in the human nose are Staphylococcus aureus (methicillin resistant strains are called MRSA) and Streptococcus pneumoniae. Typically, only one species or the other is found: they usually don't coexist in your schnozz. One mechanism that S. pneumoniae uses to displace S. aureus is to make hydrogen peroxide, but it's unclear how this actually works, since hydrogen peroxide, at concentrations which…
mikethemadbiologist | June 2, 2009A recent post about the looming specter of bioterrorism by William Lind due to 'biohacking' seems overblown to me. But before I get Lind, what I find particularly disturbing about hyping a non-existent bioterror threat is that it makes combating infectious disease--the stuff that kills millions worldwide--much harder due to unnecessary regulations and restrictions. Onto Lind:
For years, I have warned in these columns and elsewhere that the future weapon of mass destruction we should most fear is not a nuke. Rather, it is a genetically engineered plague, a plague no one has ever seen before…
mikethemadbiologist | May 26, 2009Having recently returned from the ASM (American Society for Microbiology) General Meeting held in Philadelphia, I'm convinced that it should be held there every year--or, at least, it should be the permanent East Coast venue.
When I go to a meeting, I want several things:
Stuff to do. Restaurants, museums, and so on.
Things need to be accessible. That means I have to be able to walk to them or take public transit (I don't want to have to rent a car just to leave the conference center).
Lodging needs to be close to the convention center (ASM is usually an 8,000-12,000 person meeting; it…
mikethemadbiologist | May 25, 2009Tweet? (and not the internet kind). At the recent ASM meeting, I saw a poster presented by Mark Schroeder of Ohio Wesleyan University about the prevalence of methicillin-resistant staphylococci in wild song birds (the staphylococci include several potential pathogens such as Staphylococcus aureus and S. epidermis).
Based on my notes (Note to wee lil' scientists: If you're presenting a poster, always bring lots of page sized copies. Always.), roughly ten percent of birds had staphylococci (I think they were isolated from the plumage, but I can't be certain).
Among the mannitol-positive…
mikethemadbiologist | May 21, 2009...the signal peptide? Interesting. I'll start at the beginning.
One of the few bright spots regarding the problem of antibiotic resistance is that resistance typically infers a fitness cost to the bacterium, at least initially. In other words, the resistant strain usually grows slower than a nearly identical sensitive strain*. While compensatory mutations can lower or eradicate this 'cost of resistance', it is thought that resistance can't increase initially without favorable selective conditions--antibiotic use--due to the cost of resistance.
We'll need a little background about…
mikethemadbiologist | May 20, 2009While I'm away at ASM, here's something from the archives for you
When 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-…
mikethemadbiologist | May 16, 2009I'll be off to the American Society for Microbiology meeting tomorrow. Anybody going?
The blog will keep on rolling thanks to Our Benevolent Seed Overlords Blogerrator 9600.
grrlscientist | May 7, 2009tags: TEDTalks, Laurie Garrett, H5N1 Influenza, influenza, virology, epidemics, streaming video
Recorded in 2007, as the world worried about a possible avian flu epidemic, Laurie Garrett, author of "The Coming Plague," gave this powerful talk to a small TED University audience. Her insights from past pandemics are suddenly more relevant than ever. [21:05]
mikethemadbiologist | May 5, 2009Before I get to the substance of this post, let me state that I'm not a big fan of genetically modified food crops (GMO crops). And there are few bloggers who have spent more time blogging about antibiotic resistance (never mind spending part of his professional career addressing the problem). But this claim that GMOs have led to multi-drug resistant tuberculosis is absurd:
Instead of blaming multi-drug-resistant tuberculosis on patients and their alleged non-adherence to the prescribed drug regime, it would be prudent to investigate and eradicate the underlying cause for multi-drug-…
sporte | April 30, 2009We 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 trees I got surprised me so much all sense flew out of my brain.
2. Show us the multiple alignments. Okay. I'll…