Craziest Experiments
March 31st, 2008 ecoliCracked.com has another great article… the 10 craziest science experiments ever conducted. Some are cool, others are stupid. It’s an interesting read either way.
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pap operon in Uropathogenic Escherichia coli
March 26th, 2008 ecoliSo I’m giving a journal club presentation in about an hour (as of 6, when I started this) and I figured I’d write a quick blog post about it.
The urinary tract is a multi-organ system that opens to the external environment and, as a result is prone to infections from various pathogens. Approximately 50% of women will get at least one urinary tract infection (UTI) in their lifetime. Uropathogenic Escherichia coli (UPEC) is responsible for 80% of community acquired UTIs, so it is an important pathogen to study.
There are essentially four stages in the current UTI model. Attachment of UPEC to the walls of the urinary tract, invasion of host epithelial cells, replication within those cells, and exfoliation of the epithelial cells concurrunt with bacterial efflux.
My presentation is primarily concerned with the first stage of this process, namely attachment or adherence. UPEC adhesion to the cell wall is absolutely required for initiation of infection, which makes adhesins molecules attractive candidates to study, for the ultimate purpose of vaccine creation. In addition to initiating infection, adherence prevents mictruition, or the ‘washing out’ of UPEC by urine flow throughout the urinary tract. Another important factor is that these adhesin proteins can act as surface antigens and be recognized by the host immune system.
Evading immune response would then become a primary ‘goal’ of UPEC, from selection pressures from the immune system. There are several homologous types of adhesins, and each has various roles in the infection process. In a multi organ system, a bacteria may want to express different adhesins at different times. This would help the organism adapt to microenvironments and conserve resources by limiting coexpression. In addition this could help UPEC evade host immune response by ‘hiding’ key surface antigens. This is known as phase variation.
I’m primarily concerned with a specific adhesin known as pyelonephritis-associated pili (Pap). These pili bind to uroepithelial cells and are responsible for symptomatic UTIs. The expression is controlled by a single operon (promoter, operator, structural gene sequences). UPEC contain several homologous copies of this operon, which have variation in their function.
So, we know that phase variation can control the expression of analogous adhesins, because the gene expression is regulated by different mechanisms. But, homologous copies of the pap operon are controlled by the same mechanism, even though they can have slightly different functions. How can a bacterium control the expression of these different pap operons?
The answer lies in the their very sequence variation. Sequence variation in the genes that encode their epigenetic regulators is selected for. These variation changes the functioning of the epigenetic proteins so that the expression can be modulated or the gene activators turned off. The expression of some copies of the operon are favored, and this is selected for by the host immune system.
References:
Makrina Totsika, Scott A. Beatson, Nicola Holden, David L. Gally (2008) Regulatory interplay between pap operons in uropathogenic Escherichia coli , Molecular Microbiology 67 (5) , 996–1011
Beards: wisom vs. microbes
March 25th, 2008 ecoliSo what’s with academics infatuation with facial hair? I suppose its perhaps less common these days, but facial hair is certainly more commonly seen in universities than on the street. Jake Young’s theory (from Pure Pedantry) is that it extends from the necessary slovenliness that comes with being a grad student.
In any case, having a beard can pose problems, especially for those microbiologists, because beards happen to be an excellent substrate for microbes. It then becomes as issue of balancing wisdom vs. safety.
Purim
March 24th, 2008 ecoliI don’t usually write about this type of thing, and I promise I won’t make it a habit. Mike the Mad Microbiogist brought up an interesting post the other day, related to the Jewish holiday of Purim, I felt I should share it with my readership.
Its essentially about the concept of free will and the unusual way (for a ‘Western’ religion) that Judaism deals with it.
Borrelia burgdorferi
March 21st, 2008 ecoliMy father was diagnosed with early stage Lyme disease this morning, so in honor of him I want to talk a little bit about Borelia burgdorferi.
Lyme disease was described a few decades before the cause was known. The present form became studied after outbreaks occured in the area around Lyme, Connecticut, giving the disease its popular name.
B. burgdorferi is a spirochete bacteria, meaning that it has a helical coiled shape. It was first identified by Jorge Benanch, of the State University of New York at Stony Brook, who developed the first critical ELISA antibody test that could test for the presence of the bacteria. Dr. Benanch just so happens to also be the boss of my department and his wife was one of my high school biology teachers (now there’s something wikipedia can’t tell you). Soon after it was isolated by Willy Burgdorferi, for whom the bug was named.
The life cycle of Borrelia is interesting because they require ticks for transmission and mammals to feed on. Tick larvae become infected with Borrelia during the larvae or nymph stage when they feed on white-footed mice. Borrelia remains in the tick as it advances in its life cycle to adult. The adult ticks then feed on small mammals or humans, transmitting the spirochete where (in humans and dogs) it can become pathogenic. However adult ticks preferentially feed on white-tailed deer (no immediate relation to white-footed mouse) and is the source of the name ‘deer tick.’ The adult tick has to feed on deer blood for at least three days in order to be able to reproduce. Borrelia is nonpathogenic to deer.
This is an interesting commensal/parasitic relationship between these three organisms. The ticks rely on deer and Borrelia relies on the ticks. They are barely aware of the others existence, yet they have evolved together in a unique sort of hierarchy.
Talk like a Biologist Day!
March 21st, 2008 ecoliTaking Swansont’s lead, I’m declaring an annual Talk Like a Biologist Day. As far as I know, there is no such day already, so I’m going to take the initiative in saying that there needs be one. The date is as yet to be determined, but some possibilities are April 22nd (Earth Day) and July 18th (birthday of Robert Hooke, discoverer of the cell). Leave a comment if you like one of these two dates, or you would like to propose a different one. This is a collaborative work in progress, so don’t be shy.
So in order to talk like a biologist, you’ll need to become familiar with the jargon and how to use it in every day situations. Allow me to provide some examples and feel free to add your own.
Is something distracting you from getting your work done on time? Don’t worry, it’s not your fault, it’s just due to an “allosteric interaction.”
Any type of regular route is a “pathway.”
Don’t talk about how someone looks, but you should discuss their “phenotype.”
Tough day at the office? If you snap at your co-workers, blame it on negative “environmental stimuli”
If something is happening here, it’s “autonomic.” Far away is “somatic.”
Murdered your child in a fit of frustration? Don’t worry, just pass it off as “strategic infanticide.”
Don’t pick out your outfit this evening, “apply selection pressures” to your wardrobe.
You’re not over the hill, you’re just in the ’stationary phase’ of your growth.
Trying to leave work early? Tell your boss that due to the “high concentration” of employees, you’re “diffusing” out of the building and that attempting to stay would be “energetically unfavorable.”
Put “saccharides” in your coffee.
Try to “replicate your design information” with your significant other tonight.
While your at it, assure them that s/he has your “striated involuntary cardiac muscle tissue.’
Don’t touch anything today, but “probe” with your “receptors.”
Refer to household pets by using their binomial nomenclature, and don’t forget to refer to yourself as a “taxonomist.”
If you happen to be stacking objects today, make sure everyone knows that its a “nested hierarchy.”
Don’t forget to take it easy today. On Talk Like a Biologist Day, its important to “maintain homeostasis.”
H. pylori - the story of stomach ulcers
March 20th, 2008 ecoliHelicobacter pylori is a fascinating bacteria with an interesting historical timeline. The Microbiology Blog ran a little segment on it, to announce an upcoming book, and I thought I’d add to the story.
Back in the days before 1979, stomach ulcers were blamed entirely on spicy food and stress. People that came down with ulcers or gastritis were put on a bland diet of oatmeal and soft foods like that.
Enter Australian pathologists, Robin Warren and Barry Marshall. They successfully isolated and cultured H. pylori from mucosal linings of the stomach specimens. They suggested that it was H. pylori in fact, and not diet, that was the direct agent of stomach ulcers and gastritis.
Initially, the response of the scientific community was skepticism. The consensus was that no organism could survive the high acidity of the stomach (pH 2). However, in an astonishing experiment, they proved the entire scientific community wrong.
Dr. Marshall drank H. pylori cultures, subsequently developing gastritis and the organism was recovered from his stomach lining. After ten days, an endoscopy was taken proving his symptoms were, in fact, gastritis and that H. pylori was present. He then treated himself with bismuth salts and Metronidazole, antibiotics to anaerobic organisms. They went on to show antibiotics as an effective treatment for many clinical cases of stomach ulcers.
To make the case even more interesting, in turned out, from later DNA sequencing data, this organism represented an entirely new genus of bacteria. Of which, several other species were discovered in other mammals and birds.
For their work and obvious dedication to ‘hands on’ experimentation, Warren and Barry received the 2005 Nobel Prize in medicine.
*disclaimer: drinking bacterial cultures will not necessarily garauntee a Noble Prize, though if you’re really desperate, it might be worth a try*
Battlefield Acupunture
March 19th, 2008 ecoliOrac, from science blogs’s Respectful Insolance, brings to light a disturbing new trend in medicine; Woo invades the military.
Apparently, some German and American medics are (independently) exploring the use acupuncture to deal with pain. Despite the enthusiasm the military seems to have for this new program, they don’t seem to care much about waiting for research to discover if acupuncture is actually does what they say. It seems like this could be a potentially expensive and dangerous display of the placebo effect.
Ask Col. Richard Niemtzow, a radiation oncologist-turned acupuncturist for the Air Force how to deal with phantom pain of amputees and he’ll tell you to put needles into the ear, an organ closely associated with the central nervous system. The needles interfere with pain processing by interrupting and turning “the pathways.”
Filamentous Bacteria
March 18th, 2008 ecoliOriginal ideas that categorized filamentous bacteria as the stressed and dying members of a population are apparently wrong. This is not a terribly unusual finding since scientists are always correcting ideas; assigning roles to presumably defunct systems and finding mechanisms for what were thought to be random processes.
Filamentation in bacteria occur when the cell continues to grow after its chromosomes have been copied, but the cell doesn’t divide. Filamentous cells are characterized by their elongated shape, which can be 10-50 times longer than normal. Certain bacteria have genes that encode proteins which can make alterations to cell length for the purpose of becoming filamentous, but random mutations can cause deletions in components controlling cell division with a similar affect.
Human Evolution & History: A Complete Theory [?]
March 18th, 2008 ecoliMy last few entries have relied on a specific idea that, given a group of non-kin cooperating individuals, the ability to cheaply coerce cheaters is unique to humans. This idea may be the strongest evidence we have for the evolution of human social and sexual behavior., according to this paper, by Dr. Paul M. Bingham.
When multiple remote killing animals kill or threaten simultaneously, they achieve an unexpectedly large decrease in the cost or risk of enforcing individual self-interest. This requirement for simultaneity means that this strategy is viable only when the common, congruent, and thus, cooperative self interests of large numbers of individuals are engaged.
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