microbiology
sa smith | October 12, 2014On an academic level, I am not a fan of bacteria. I like viruses. Thus, I usually like the idea of using viruses to kill bacteria. But I am a huge fan of fecal bacteriotherapy, aka, poop transplants.
Someone is sick, they get antibiotics. Antibiotics kill off their 'normal' bacteria, and allow 'bad' bacteria, like Clostridium difficile, to thrive. C. diff is a dangerous, increasingly drug resistant bacteria that kills, according to Wikipedia, 300 people a day.
Fecal bacteriotherapy is replacing the C. diff patients good bacteria with gut bacteria from someone else. Gut bacteria, normally…
tsmith | November 21, 2013Now that seemingly the flu outbreak storyline has been wrapped up on The Walking Dead (unsurprisingly, but disappointingly, with their ineffective treatments proving to be miracle cures), there's still one more zombie microbiology topic I'd like to cover: what's up with the bite, and is it the cause of death? I said previously:
"We know the pathogen can certainly be spread by bites and then cause zombification that way..."
but one commenter disagreed, noting:
"I don’t think we have evidence for that from the show. I think it clearer that zombie bites cause death, and there doesn’t seem to be…
tsmith | November 5, 2013(As previously, spoilers abound)
So on this week's Walking Dead soap opera, we find that Daryl/Michonne's group is still out and about searching for medical supplies. Back at the prison, the food situation is dire (apparently all the food stores were in the cell block where the infection broke out), so Rick and Carol head out to look for both medicines and food from the local 'burbs. During their outing, discussion ensues of Carol's attempt to stop the prison's apparent influenza outbreak by killing two people who, at that point, were the only ones showing symptoms of disease. Rick decides he…
kbonham | September 3, 2013A little over 4 years ago, I joined up with three friends from grad school and launched a brand new science blog, "We, Beasties!" The name was meant to be a play on a phrase from Paul de Kruif's somewhat tongue-in-cheak translation of the first-ever microbiologist Antonie von Leeuwenhoek's term "Animacules." von Leeuwenhoek was the first human being to glimpse the world of life invisible to the naked eye, and de Kruif, 400 years later, dubbed those minuscule replicators "wee beasties." Of course, we now know much more about our microbial companions, including their immeasurable impact on our…
kbonham | June 12, 2013A couple of weeks ago, I gave a talk for
Tonight, I'm presenting at the Science In The News (SITN) Spring lecture series. If you're in the vicinity of Boston, you can come watch at 7pm in Pfizer Auditorium, located in the Mallinckrodt Chemistry Lab, 12 Oxford Street, Cambridge MA 02138.
If you can't show up in person though, SITN is now broadcasting live via google hangouts. Check out this page for details, and I'll try to upload the video feed here around 6:30 ET.
Start about 22min in
kbonham | January 21, 2013[This question was originally asked on www.reddit.com/r/askscience on Jan 17, 2013]
Why do microorganisms only begin breaking down our tissues after death? What stops them from doing so whilst we are still alive?
The main reason is that our body maintains a multitude of barriers that largely prevent bacteria and other microorganisms from gaining entry. The first and most obvious of these barriers is the skin, but there are also similar barriers along all of your mucosal surfaces (gut, ear, genital tract etc). These barriers consist of cells that are knit together incredibly tightly (google:…
kbonham | December 22, 2012[This past fall, I taught a course at Emerson College called "Plagues and Pandemics." I'll be periodically posting the contents of my lectures and my experiences as a first time college instructor]
Most of this post was written back in September, when it still seemed possible that I would be able to teach the class, write the blog and do science. Please forgive any anachronisms that I failed to purge.
Last time, I talked about what science is and why it's awesome. This is the first half of lecture 2, which was originally given on 11 September, 2012.
Lecture 2a (reading: Zimmer - The Tangled…
sa smith | December 3, 2012*sigh* Two years ago, this time, I was packing my bags for Antarctica. *sigh*
As much as I would like to go back, I could never afford it... so I need to figure out how to get on one of these research teams working in Antarctica.
See, abiogenesis, life on other planets-- that is not just a thought game physicists play. There are scientists-- microbiologists, virologists, biochemists, geologists-- who try to find and study life in the most extreme locations on Earth, to try to figure out what 'life' could look like say, on Mars, or Europa.
Its not a game.
Its the research they perform day-in-…
sa smith | September 26, 2012Its like, instead of 'Put a bird on it!', scientists are like 'Put a virus on it!'
Got cancer? Put a virus on it! In constant pain? Put a virus on it! Addicted to cigarettes? Put a virus on it! Genetic disease? Put a virus on it!
Got acne? Put a virus on it!
Propionibacterium acnes Bacteriophages Display Limited Genetic Diversity and Broad Killing Activity against Bacterial Skin Isolates
YAY!!!
Acne, though not life-threatening, sucks.
If you dont have acne, consider yourself lucky. Some people can get it relatively under control with a combination of over the counter meds and…
sa smith | August 1, 2012The Evolutionary Consequences of Blood-Stage Vaccination on the Rodent Malaria Plasmodium chabaudi
The concept of vaccination is, superficially, simple-- Safely mimic 'infection' so your immune system learns how to fight a pathogen, without needing to get sick from the genuine pathogen. Then if you are ever exposed to the real, scary pathogen, your immune system already knows how to deal with it.
But things dont always go according to plan...
In 1966, a novel vaccine against Respiratory Syncytial Virus was a tragic failure. The lucky kids didnt respond at all. The unlucky kids made a…
sa smith | July 18, 2012WARBLEGARBLE!!!
Fighting malaria with engineered symbiotic bacteria from vector mosquitoes.
Malaria kills 1.24 million people a year. Mostly babies under 5 years old.
Malaria is becoming resistant to our drugs.
We cant figure out how to make an anti-malarial vaccine.
We can make GMO mosquitoes that are resistant to carrying malaria, but we dont know how to implement them in nature.
NEW IDEA: Make GMO bacteria that make mosquitoes resistant to malaria colonization. 'Bait' wild mosquitoes with sugar water filled with GMO bacteria. See a potential 84% decrease in mosquitoes carrying malaria,…
milhayser | June 9, 2012Spring is in the air, and Clostridium tetani is in the earth. On Casaubon's Book, Sharon Astyk writes "with playing in the dirt comes minor injuries that you really don’t want to turn into anything nasty." Infection through open wounds can be fatal, as the bacterium releases a neurotoxin that causes uncontrolled muscular contractions. So if it's been ten years or more since your last vaccination, now is a good time for a booster. Meanwhile, Dr. Dolittle shares the amazing winning images of the inaugural Bio-Art competition on Life Lines. From the discharge of electric fish to the…
milhayser | June 6, 2012On Earth Day, Greg Laden took the opportunity to thank BP for the “modifications made to the ecosystem of the Gulf of Mexico” by the Deepwater Horizon oil spill. Surviving specimens of coral “have been provided with hip new color schemes (mainly black and blackish),” while creatures such as shrimp and crabs exhibit physical deformities “which will surely make them easier to catch and, according to BP, does not affect their edibility.” Crude oil is organic, after all, as Kevin Bonham reminds us on We Beasties. He says “it turns out that nearly million barrels of oil naturally seeps out of the…
kbonham | April 20, 2012Yesterday on Marketplace, there was a great piece by Alex Chadwick on the fate of all the oil released during the BP oil spill two years ago.
Oil is a product of organic matter that was deposited many, many years ago. It's gone through many, many changes deep in earth under high pressure, high temperature -- but fundamentally it's an organic material.
This is hard to grasp. Oil is food, an organic buffet for microbes. So, two years ago, when the BP oil plumed in the water, very soon the bacteria plumed, too. Different kinds in different parts of the ecosystem -- deep water, shallow, shoreline…
jtoney | February 19, 2012
Ice 9 by toastforbrekkie.
The idea of Ice-9, although fictional, has always fascinated me. Its properties are so powerful, so influential, that one "seed crystal" can direct its entire surroundings, freezing oceans. A recent discovery of one component of the cell wall of bacterium reminded me of this effect. Let me explain.
First:
Ice-nine is a fictional material appearing in Kurt Vonnegut's novel Cat's Cradle. It is supposed to be a more stable polymorph of water than common ice (Ice Ih) which instead of melting at 0 degrees Celsius (32 degrees Fahrenheit), melts at 45.8 °C (114.4 °F…
sa smith | February 8, 2012Frequent readers of ERV, or SciBlogs in general, are used to vitamin/mineral woo. "Megadoses of Vitamin C cures EVERYTHING!" "Vitamin D is better at preventing the flu than the VACCINE!" "Zinc cures the COMMON COLD!"
What we are used to dealing with, is snake-oil salesmen looking to sell their particular bottled garbage to people with medical anxieties/paranoia (but are otherwise healthy individuals) with disposable income.
But the world is not full of rich Westerners paranoid about The Big C.
There are lots of people on this planet who struggle to get themselves and their children…
jtoney | February 1, 2012
Color-enhanced scanning electron micrograph shows splenic tissue from a monkey with inhalational anthrax; featured are rod-shaped bacilli (yellow) and an erythrocyte (red)
Credit: Arthur Friedlander
A university professor has allegedly mailed anthrax to the Pakistani prime minister's office in October, accoding to today's The New York Times. Could this be the beginning of a new anthrax scare? Is history repeating itself?
If true, any individual considering such "attacks" can no longer assume that their weapons are untraceable, as shown by the anthrax scare in 2001.
Below is an excerpt…
sa smith | October 13, 2011Me, September 1, 2011:
Black Death not initiated by a plasmid? My money is on a moron.
Phages can encode for gene groups called morons.
I am not joking.
These are viral genes that dont code for anything the virus wants, like structural proteins, or enzymes the virus needs-- They are genes that make having the virus around attractive to the bacteria. And few things are more attractive to a pathogen than making you sick, thus spread the bacteria faster than if you werent pooping/oozing/puking/etc.
I bet its a moron.
Nature, October 12, 2011:
A draft genome of Yersinia pestis from victims of the…
sa smith | September 1, 2011What caused The Black Death?
Its not only an interesting question from a paleomicrobiology standpoint, but of practical importance-- While we have all kinds of technology here in 2011 that would have, no doubt, increased the survival rates of Plague victims in the 1400s, it would be more comforting to know exactly what caused that epidemic and why so we can be 100% prepared for it (or something similar to it) in the future.
One theory is that the Black Death was caused by a bacteria, Yersinia pestis. Weve got Yersinia pestis around today, but what made the Black Death Yersinia pestis really…
mikethemadbiologist | August 24, 2011By way of Matthew Yglesias, we read that,over at National Review Online, Kevin Williamson claims progressives only care about science as a way to wage culture war (yes, coming from movement conservatives, that's rich):
There are lots of good reasons not to wonder what Rick Perry thinks about scientific questions, foremost amongst them that there are probably fewer than 10,000 people in the United States whose views on disputed questions regarding evolution are worth consulting, and they are not politicians; they are scientists. In reality, of course, the progressive types who want to know…