microbiology
sporte | April 29, 2009I'm teaching an on-line bioinformatics course this semester for Austin Community College. They are in Texas of course, but I am in Seattle. This presents a few interesting challenges and some minor moments of amusement.
Today, the school sent all the faculty emails telling us to stay home if we're sick.
Got it. If I think I have flu, I will not fly to Texas.
Instead, I'll stay home and watch videos on coughing without contaminating others.
Watch "Why don't we do it in our sleeves?" and find out how you rank on the safe coughing scale.
grrlscientist | April 29, 2009tags: Antigen Shift, Influenza Viruses, molecular biology, virology, microbiology, streaming video
This video discusses the process of antigen shift in influenza viruses, such as the H1N1 "swine flu" that has recently been identified in Mexico and in quite a few other countries, including in NYC [1:18]
mikethemadbiologist | April 28, 2009Since TEH SWINE FLU!!!11!!! is a hot topic, I thought this post about how infections could evolve increased virulence after switching animal hosts was relevant. From the Murky Depths of the Mad Biologist's Archives: There's no reason to think that an epidemic influenza strain won't become more deadly....
Several people have argued that if an influenza pandemic were to occur, it will rapidly evolve to become less virulent--that is less deadly. A recent paper explains why this might be wrong.
Basically, the flaw with the 'optimistic' argument is that it is assumes that the virus will be…
bioephemera | April 27, 2009
This air purifier ad from Sharp is a little creepy, in a Spongebob Squarepants way. I love how you can see their fluorescent organelles! Unfortunately I don't see anything here that resembles a virus, but with swine flu all over the news, this serves as a good reminder to wash your hands.
Ad by Takho Lau for ad agency M&C Saatchi of Hong Kong. Found via Next Nature
sporte | April 22, 2009That's how new life forms are created every day in the wild, folks. Human researchers of course have added a few twists on the theme. If we can't induce bacteria or animal cells to collect new bits of DNA on their own, we turn to electroshock therapy. With plants.... aw heck, we just shoot them.
And where did this crazy rant come from you ask? Last Saturday morning, at the crack of 9 am I got to be interviewed on a radio program with two of the main spokespeople from the DIY bio movement, Mackenzie Cowell and Meredith Patterson.
The program was "The Food Chain" (you can listen to it…
mikethemadbiologist | April 21, 2009A while ago, I talked about some things biologists should learn, and the glaring omission was mathematical fluency. I bring this up because one of the things the Mad Biologist does is work on the Human Microbiome Project (between that, and fighting evil, we are very busy...). The part of the Human Microbiome Project ('HMP') that I'm involved with is a consortium of four sequencing centers and an informatics center, whose goal is to sequence the microbes associated with 18 different body sites from 250 people. And math is vital to what we do.
Before I get to the reason why math matters,…
mikethemadbiologist | April 17, 2009A recent article in MMWR Weekly with the unassuming title of "Preliminary FoodNet Data on the Incidence of Infection with Pathogens Transmitted Commonly Through Food --- 10 States, 2008" is incredibly disturbing.
The incidence of reported (more about that in a bit) Salmonella was 16.20 cases per 100,000 people. If we use a population size of 300 million, that means (Mad Biologist takes off shoes to do big number arithmetic) roughly 48,600 people had food associated Salmonella infections.
But it's probably higher than that, although I have no idea how much higher. For a Salmonella infection…
grrlscientist | April 16, 2009tags: bacteria, microbiology, TEDTalks, science, streaming video
This interesting video is a TEDTalk. TED -- for Technology, Entertainment, Design -- talks cover these topics as well as science, business, development and the arts. They are 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. In this TEDTalk, Bonnie Bassler discovered that bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning…
grrlscientist | April 8, 2009tags: microbiology, astrobiology, new species, Indian Space Research Organization, bacteria
Bacterial colonies.
Image: Hub Testing Laboratory [larger view].
According to a recently published press release, three new species of bacteria have been discovered in the upper stratosphere by Indian scientists in an experiment conducted by the Indian Space Research Organization (ISRO). This discovery lends some credence to the hypothesis that life might have originated elsewhere in the cosmos and was seeded on Earth after colliding with a foreign body, perhaps a comet or asteroid, that was…
mikethemadbiologist | April 6, 2009I recently wrote about the introduction in the House of the Preservation of Antibiotics for Medical Treatment Act (PAMTA). This is a really critical piece of legislation that could put a dent in the evolution of resistance. Now, there's more good news.
Senator Kennedy, along with Republican Senator Olympia Snowe, has introduced a companion bill, S. 619. Again, I can't stress how important this legislation is. Among other things, it moves the burden of proof to drug manufacturers, forcing them to demonstrate that a drug is vital. It also redefines 'therapeutic use' in such a way that it…
mikethemadbiologist | March 22, 2009Always listen to the Mad Biologist. By way of Joe Windish at The Moderate Voice, we find out, just as I predicted, that the pork lobby would claim we don't know enough about the MRSA ST398 problem:
Livestock scientists call the opinion piece "highly speculative", and point to the Centers for Disease Control and Prevention (CDC) statements on MRSA that say most if not all cases of MRSA come from person to person contact, not person to animal. The column also does not define this strain as one that is found on any swine farm in the vicinity of Camden, Ind.
"They are making a huge leap…
sporte | March 21, 2009Cofactor Genomics is offering to sequence a genome for a few classes for free using Next Generation DNA Sequencing technology (either Illumina GA or via AB SOLiD).
Quoting from their site:
Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project could be used as an effective teaching aid in their class. We will review and choose the best entries during the month of May. Those entries will be awarded a free sequencing project including project experimental design, sample QC, library construction, sequencing, and computational analysis. Those projects…
mikethemadbiologist | March 16, 2009I'm always loath to criticize mainstream discussions of the antibiotic resistance, particularly when the link between antibiotic use in agriculture and antibiotic resistance is raised. But, while NY Times columnist Nicholas Kristof meant well, he missed the mark.
In his column about MRSA ST398, he describes things that might happen. Here's one example:
Public health experts worry that pigs could pass on the infection by direct contact with their handlers, through their wastes leaking into ground water (one study has already found antibiotic-resistant bacteria entering ground water from hog…
mikethemadbiologist | March 12, 2009Nicholas Kristof has an interesting op-ed in the NY Times about the relationship between pig farming and MRSA. I'll be curious to see what he writes about in his next column, since he says, "This is a system that may help breed virulent "superbugs" that pose a public health threat to us all. That'll be the focus of my next column, on Sunday."
I feel somewhat vindicated since this is a drum I've been beating for a long time; I've also been involved in efforts to curb the use of the antibiotic cefquinome in agriculture.
The other good thing is that ScienceBlogling Tara, who has published on…
terrasig | February 20, 2009While I get to finishing my post on the much-ballyhooed ScienceOnline'09 winetasting, I'd like to share with readers a fantastic wine essay by MIT Professor of Science Writing and multiply-decorated journalist, Thomas Levenson. Tom also writes The Inverse Square Blog where each post includes at least one illustration as beautiful as his writing. Tom is also author of the upcoming book, Newton and the Counterfeiter: The Unknown Detective Career of the World's Greatest Scientist, currently scheduled for release on 4 June 2009.
I had the lovely pleasure of sitting between Tom and Rebecca Skloot…
mikethemadbiologist | February 8, 2009Before I get to the ongoing calamity, the economic impact of a nation-wide viral epidemic in horses in 1872 is worth considering (italics mine):
During the late 19th century, the American economy relied on horses the way it depends on gas today. Horses unloaded cargo from ports, transported goods from city to city, worked the farms, supported the army, and served as the emergency vehicles of choice. Without them, the American workforce would have ground to a halt.
And that's exactly what happened in 1872, when an estimated 99 percent of all horses in America contracted equine influenza. The…
mikethemadbiologist | January 24, 2009
I'm kidding, but ScienceBlogling Tara Smith has co-authored a PLoS One article about the emergence of the MRSA strain ST398 in Iowan pork farms. Pig farms are a tremendous reservoir of bacteria: as far as I can tell, there are about six pigs for every person in Iowa.
MRSA ST398 a methicillin resistant S. aureus bacterium that has spread epidemic through various European animal populations (particularly pigs). It recently jumped from the animal population to the human population in Europe and has begun to establish itself there in hospitals. The last thing we want is for another MRSA…
mikethemadbiologist | January 13, 2009The emerging MRSA strain ST398 has found a new home--chickens.
MRSA (methicillin resistant Staphylococcus aureus) was first found to have swept through European swine herds from 2003-2006. Then it entered the hospital system.
In the U.S., it had not been observed in agriculture until very recently (it's ScienceBlogling Tara's fault--on a serious note, she studies this critter). It hasn't been seen in hospitals in the U.S. yet.
What's disturbing is that a recent study from Belgium indicates that MRSA is on the rise in chickens and that it's due to ST398 (this isn't a trivial thing; most…
sporte | January 12, 2009
The 2009 Summer Research Experience for Undergraduates in Environmental Microbiology at UNLV is now accepting applications. This NSF supported program provides undergraduates with an opportunity to perform independent research under the guidance of a faculty mentor.
Students will collaborate with faculty mentors in developing and carrying out hypothesis-based projects on microorganisms from diverse habitats such as hot springs, the deep terrestrial subsurface, hypersaline lakes, arid soils, and ephemeral water sources. Students may also choose to explore the mechanisms of magnetotaxis,…
sporte | January 1, 2009The other day, one of my commenters stated that "a well-informed sixth-grader should be able to distinguish between MRSA and E. coli".
Here's a nutrient agar plate with some of the bacteria that we isolated from a local creek last fall. We identified our bacteria by sequencing the 16S ribosomal DNA, but for various reasons, that I won't go into here, we don't know which sequences belong to which colonies.
Figure 1. Bacteria isolated from a local creek.
I guess we need some well-informed sixth graders. ;-)