General Epidemiology
tsmith | June 13, 2006 Sometimes it's amazing just how little we know about the microbes around us. For precious few microbes, we know a good deal about virulence factors--genes and proteins that, when present, increase the severity of disease either in animal models or in humans (or both). However, much of this research has been done investigating acute infectious diseases, where one is infected, becomes ill, and gets better in the course of a few weeks to a month. Much less is known about factors that affect long-term (or chronic) infection. A recent study addressed one gap in this research, examining what…
tsmith | June 9, 2006I wrote recently how evolution and phylogenetic analysis of HIV isolates has provided evidence that the progenitor to HIV jumped into humans in Cameroon or a nearby area. Obviously it's a topic that's interesting to me, but may seem a bit esoteric to some. RPM over at Evolgen has a new post showing another application of phylogenetic analysis to HIV that may be of interest to readers here, where infectious disease epidemiology meets CSI.
tsmith | June 9, 2006Over at Doc Around the Clock, Dr. IBear has a nice post on Lyme disease: what it is, what it's not, and how to deal with ticks (appropriately, not as his mom removed them). He mentions this:
Most of the time people who get Lyme disease don't even know or remember being bitten by a tick. Thus, it stands to reason that if you do remember being bitten by a tick you probably don't have Lyme disease.
I want to elaborate on this just a bit, below.
A reason many people don't realize they've been bitten is because when the tick bites the human to transmit the Borrelia spirochete, it's not always a…
tsmith | June 7, 2006 A recent story detailing an outbreak of sexually-transmitted diseases has gotten a good deal of attention from news outlets and blogs. The reason it's newsworthy is because the individuals affected aren't teenagers or single twenty-somethings; they're senior citizens. So, let me point out the obvious: even "old people" have sex.
This sometimes uncomfortable fact of life was driven home to me when I was just a teenager myself, when my grandma was discussing the difficulty she had showering (she'd just had surgery). Someone had asked whether grandpa was much help, and she mentioned that…
tsmith | June 7, 2006Antibiotic resistance gets a lot of attention, but it's not the only kind of drug resistance that's of concern. Derek of In the Pipeline has a post up discussing resistance to cancer therapies.
tsmith | June 5, 2006Yesterday, the New York Times op-ed by John Moore and Nicoli Nattrass discussing denial of HIV. They also featured an article suggesting that more human-to-human transmission of H5N1 has occurred than previously thought.
tsmith | June 5, 2006Liam Scheff has now turned his attention from HIV to avian influenza, with predictable results. Analysis below...
Scheff's self-stated goal is to "...review some of the bright and shiny inconsistencies that have come into view on the bird flu." However, he's not exactly consistent himself, ranging from minor errors to total contradictions of his own words. He starts off discussing "stray cats and Chinamen:"
In March, 2006, The Associated Press reported: "In Austria, state authorities said Monday that three cats have tested positive for the deadly strain of bird flu in the country's…
tsmith | June 2, 2006John Hawks highlights a new article in today's Science, Metagenomic Analysis of the Human Distal Gut Microbiome. This goes nicely with the posts here recently on the topic of how our microbes affect our health and weight (part I; part II). A bit of discussion of the new article below...
First, I want to briefly mention what "metagenomics" means. There's a nice overview of it here on wikipedia. Basically, instead of sequencing and assembling a genome one at a time, you take a raw sample (such as dental plaque, sea water, soil, or fecal material, in this case), isolate the DNA, sequence it…
tsmith | May 31, 2006 It can't be said often enough that "nothing in biology makes sense except in the light of evolution." Moving from physical characteristics--color, bone shape, the form of bacterial cells--to genetic characteristics in order to classify organisms--and infer phylogenies--was a giant advance. That the molecular characteristics confirmed what was known using physical characteristics was a breakthrough, and allowed for more sophisticated analyses of organisms that don't have bones or other easily-observable physical features that allow for simple classification into groups: microbes. I've…
tsmith | May 31, 2006I'm dealing with my own little epidemic (daughter managed to catch the stomach bug that's been going around her school, meaning she has to miss her last day as a kindergartener, poor thing). I found one post in the queue that I forgot to publish earlier in the month, so today won't be completely dead. In the meantime, allow me to point you to some excellent flu posts by DemFromCT at the Daily Kos:
Flu Basics: Science And Threats (a nice introductory primer).
Flu Basics II: Politics and Players.
H5N1: A Teachable Moment, And An Open Letter. This is a very good post overall, but the most…
tsmith | May 30, 2006Busy today, so sequels are on tap. There's an interesting story from Nature news that's a nice follow-up to this recent post on how microbes can influence weight. More after the jump.
Scientists have identified a key microbe in our guts that helps us glean more calories from food. The discovery backs the idea that the type of microbes in our gut help to determine how much weight we gain, and that seeding the intestine with particular bugs could help fight obesity.
Samuel Buck of Washington University in St Louis, Missouri, and his colleagues focused on one microbe called…
tsmith | May 30, 2006Leftover from last week's zoonotic diseases course: I do sometimes get away from the hind end of animals.
http://img.photobucket.com/albums/v164/roland98/IMG_6134_JPG.jpg"
tsmith | May 26, 2006Species of the bacterium Clostridium have long been a scourge of humans. They are gram-positive, spore-forming bacteria that can be found in the soil around all of us. The spores then germinate when exposed to anaerobic conditions.
Clostridium botulinum is the cause of botulism, a serious and potentially fatal paralytic illness often caused by ingestion of contaminated foods. More recently, the bacterium has been used as the source of that anti-wrinkle miracle, BoTox: botulinum toxin type A, allowing all of Hollywood to smile without a wrinkly forehead (ah, the wonders of nature!).…
tsmith | May 25, 2006I write a lot on here about evolution, and more about epidemiology. A recent article in Emerging Infectious Diseases discusses a unique combination of the two: 2,500-year Evolution of the Term Epidemic. I've said before that I'm about the farthest thing from a language scholar you can find, but it's an interesting article tracking how the usage of the term has changed since the time of the ancient Greeks.
tsmith | May 25, 2006I feel a bit guilty. I still get occasional comments on this post about the outbreak of chikungunya on several islands in the Indian Ocean. Since I'm obviously not involved in the actual outbreak investigation, all I have to offer is news reported elsewhere--and it's not exactly been a landslide of information. However, Nature does have some news to offer, based largely on a new paper published in PLoS Medicine (summary here).
Previously, the complete genomes of three isolates of the virus had been determined. Two were from strains isolated in 1952 during the first known Chikungunya…
tsmith | May 24, 2006Are we always sticking swabs up animals' asses? Why, yes we are.
(More below the fold)
My colleagues teach a summer course on zoonotic diseases. Since influenza is something we study, today we watched (and a few participated in) some wildfowl swabbing and banding. Above is the former: taking a cloacal swab from a duck. Though these were just for demonstration, this is one way to collect circulating avian influenza viruses.
We also headed out to some marshes to round up and band geese.
This one had 4 adults and I think there were 8 juveniles. We surrounded the pond; the goal was…
tsmith | May 21, 2006Or Saturday roundup, belated. Some interesting stories I didn't have time to cover:
The HPV vaccine, aimed at reducing the incidence of cervical cancer, has moved a step closer to approval.
The Institute of Medicine calls for more research into and oversight of vitamin supplements.
Continuing debate over "The Hobbit."
New research might eventually bring breathalyzers to your doctor's office. Not necessarily for alcohol.
An interesting study of experimental evolution: selecting for heat-tolerant bacteria over 1500 generations.
Yet another use for bacteriophage: diagnosis of…
tsmith | May 18, 20065 Royal Melbourne Institute of Technology staff report brain tumors since mid-April
A Melbourne university has emptied the top floors of one of its buildings after a spate of brain-tumour cases were reported during the past month. Most affected staff worked on the top floor, raising fears that cell-phone masts on top of the building are responsible. But experts say it is far more likely to be an unfortunate coincidence.
2 additional cases have been reported since 1999; 2 malignant, and 5 benign. 6 of the 7 cases have worked in the building for over a decade, mainly on the top floor, and…
tsmith | May 18, 2006Welcome to the new edition of Animalcules!
First, a few housekeeping notes. If you note the schedule, I've not yet extended it beyond June 1st. I think that, at least for the summer months, Animalcules will be a once-monthly carnival, rather than every other week. If things pick up after that, I'll change it back to the current set-up, but that will be dependent not only on entries but also on additional hosts. So, if you'd like to host in July, August, or September, drop me a line (aetiology AT gmail DOT com) an I'll get you on the schedule.
Okay...on to the entries!
We have a few…
tsmith | May 17, 2006Blogger reveals China's migratory goose farms near site of flu outbreak
The hypothesis that migratory birds are responsible for spreading avian flu over long distances has taken another knock. Last year, an outbreak of the deadly H5N1 strain in thousands of migratory birds at Qinghai Lake in western China provided what seemed the first firm evidence for the idea. Because the lake is so remote, experts assumed infected birds had flown up from southern China.
But it has now emerged that, since 2003, one of the key migratory species affected, the bar-headed goose, has been artificially reared…