Small Things Considered

A Fastidious Bacteriophage

by Michael Yarmolinsky

Patrons of upscale seafood restaurants are given the opportunity to see that the unfortunate creatures destined for the lobster pot are waving their antennae about. Savvy customers at downscale seafood markets evaluate questionable claims of freshness by smell. A fastidious bacteriophage would welcome the opportunity to gauge the quality of a potential meal, if only it could make that assessment. I was recently reminded, in the course of disposing of old reprints, that a bacteriophage named Chi can do so. It attacks only motile strains of bacteria, and then only if the flagella are active. How is this circumspect appraisal accomplished?

Phage Chi X 220,000. Source.

It has been several years since the publication of convincing support for a mechanical model that can account for the discrimination exhibited by Chi. Why revisit it now? First, for the benefit of those who have overlooked the remarkable story of Chi’s fastidious behavior and second because I suspect that we have learned only the half of it.

What sort of phage is Chi?

Chi is a virulent, double-stranded DNA phage with a long, uneven history and a long, tapered tail ending in a single, long, kinky tail fiber. It was first characterized in 1936 in the laboratory of Félix d’Herelle, the adventurer-scientist who is jointly credited with the discovery of the viruses he designated “bacteriophages.” Chi’s genome (60 kb) has recently been sequenced (Andrew Kropinski, Kelly Hughes and Roger Hendrix, in preparation).

The initial report showed that Chi attacks only flagellated bacteria. Growth of sensitive strains on agar containing phenol, at a concentration known to prevent the development of flagella, rendered the bacteria Chi-resistant. Chi-resistance could be used to select mutants defective in flagellation. Mutants altered in several of the 44 known flagellar genes of Salmonella were subsequently selected in this way.

The flagellar organelle. Source.

What sort of organelle is a flagellum?

Flagella are long, thin, helical filaments commonly much longer than the bacterial body from which they emerge at various sites. Their somewhat flexible, sinusoidal appearance was interpreted, until the early 70s, as evidence that they act like whips, but their helicity is intrinsic and their action that of a propeller rotated by a motor embedded in the cell body. Normal rotation speeds for Escherichia coli flagella are around 6000 rpm, but a record speed, set by a vigorous Vibrio, is 100,000 rpm. Each flagellum is both a reversible motor organelle and a protein export and assembly apparatus that fabricates the external filament by extruding flagellin monomers through a central channel and adding them to the growing flagellum at its very tip.

Talmudic Question #63

by Stan Zahler

When you streak out Your Favorite Bacterium on an appropriate agar plate, the colonies reach an expected diameter and stop growing. Why?

Corollary: If you inoculate YFB in the center of an agar plate and incubate it, it would reach its expected diameter. What do you predict would happen if you touch the tip of a sterile hair to the edge of the colony, draw it out on the agar radially, and re-incubate the plate?

Our Counterintelligence Staph

by Karen Schwarzberg, Mike Gurney, and Nikos Gurfield

S. aureus biofilm formed overnight on silicon elastomer, a material
used in catheters. Bar = 10 µm. Source.

Typically, when one thinks about the commensal bacteria living with us, what comes to mind are the benefits they provide by aiding in food metabolism, producing vitamins, and preventing colonization by invading pathogenic bacteria. In undergraduate microbiology courses, students are taught that "friendly" bacteria outcompete pathogenic counterparts using a variety of strategies, ranging from blocking colonization sites to all-out chemical warfare. Today, as antibiotic resistance develops at an accelerating pace, investigating how commensal and pathogenic microbes interact might give us insight useful for developing the next generation of antibiotics. Compared to the rate of bacterial adaptation, we are slow to develop new antibiotics. Our commensal organisms are under constant selective pressure to prevent colonization of their niches by a pathogen; the pathogen is under pressure to stay one step ahead of the commensal. Consequently, there is a microbial arms race occurring at the speed of evolution. One would expect that the most successful commensals, under pressure to conserve resources, might evolve some highly effective compounds to outcompete or kill the invader. Further, such compounds would be expected to act on processes so basic to survival and/or pathogenesis that pathogenic bacteria would find it difficult to evolve resistance.

Taking Risks: ASMCUE Musings

by Amy Cheng Vollmer

Source.

After missing it for several years due to other ASM responsibilities, I had the delightful opportunity to attend this year’s ASMCUE, the ‘appetizer’ course that preceded the ASM’s General Meeting in San Diego. The sessions at the ASMCUE included Microbrew ideas, Try Something New activities, Learn Something New presentations, and a fantastic poster session, as well as several plenary talks. It was stimulating to be part of the audience for so many interactive presentations!

In thinking about the ‘take home’ lessons from the conference, I was struck by the intellectual risk taking by the conference participants—a mixed group including young faculty, experienced teachers, along with veterans like myself. Interestingly, those wearing ‘first timer’ nametags were not necessarily new to their faculty positions. Several were seasoned research faculty members who were, for some reason, motivated to come this year.

Uncovering Beauty in Proteins to Fight the Pneumococcal Fratricides

by César Sánchez

From time to time, we dip into the microbiology blog by César Sánchez, Twisted Bacteria, and, with his permission, "borrow" a post such as this one.

Streptococcus pneumoniae in spinal
fluid. Source.

This post is about pneumonia and pneumococci, fratricide at the cellular level, and a pretty protein. And there's a video too!

First things first. Pneumonia is a common disease characterized by inflammation of the lungs that can be deadly: 4 million people in the world die from it every year. Half of them are children under 5 years of age. In fact, no other illness causes more deaths of children under age 5 worldwide. However, this is a preventable and treatable disease in most cases.

Many organisms can cause pneumonia, but the usual culprits are the bacteria Streptococcus pneumoniae (or pneumococcus) and, less frequently, Haemophilus influenzae type b (a.k.a. Hib). Safe and effective vaccines and antibiotics have been developed for these infections. Unfortunately, they are not commonly available in most developing countries, where pneumonia allies with poor nutrition, other illnesses (e.g. AIDS) and lack of resources to contribute to the cycle of poverty. To know more about the impact of pneumonia on world health and what can be done about it, I recommend listening to this podcast and visiting the World Pneumonia Day website.

A Posteriori

by Elio

The 2010 ASM General Meeting held in San Diego continued a hallowed tradition dating back 110 years (a tradition spanning 57 years in my particular case, so I have firsthand knowledge of more than half of this history). The meeting format changed dramatically in the 1970s when poster sessions were added. This allowed the use of many more meeting rooms for symposia and colloquia, and practically did away with the old 10 minute oral presentations that most people did not find particularly exciting or informative. This newer format (not so new to most of the readers of this piece) permits to invite “big names,” which translates to fewer oral presentations but those tending to be given by leading experts. The quality of these sessions was high this year, as it has been for some time now. Of course, everyone faced the old dilemma of wanting to attend two sessions simultaneously. After far more than 110 years of trying, nobody has managed to be in two different places at the same time (although I wouldn't put it past future technology to take care of this problem. And I don't mean videotapes!)

Source.

A special paper, one from among the many that I found exciting? A presentation by Pat Keeling from the University of British Columbia on a microsporidium of the genus Encephalitozoon that holds the current record for the smallest known eukaryotic genome: 2.3 Mbp!

Small Things: First Responders to Oil Spills

by D. Jay Grimes and Ronald M. Atlas

DAPI-stained bacterial cells attached to oil droplets
from the Deepwater Horizon site. Source: Jay Grimes.

On April 20, 2010, an offshore oil drilling rig in the northern Gulf of Mexico, the Deepwater Horizon (DH), exploded from undetermined causes. The floating rig sunk two days later, breaking off the well pipe and spilling huge amounts of oil. At the low end of the estimates, the spill has already eclipsed the 11 million gallon from the Exxon Valdez in 1989. Before the oil stops flowing the amount released into the Gulf may well exceed the 140 million gallons released into the Gulf of Mexico by the 1979 Ixtoc-1 well blowout.

The first research vessel on site was the R/V Pelican. More recently, both BP and NOAA have sent research vessels to the site. The Pelican cruise, using fluorometer readings that measure colored dissolved organic matter (CDOM) which is a surrogate for oil and dispersed oil, revealed several plumes or lenses of CDOM in the deep ocean at 700-1,300 meters; water samples from these plumes are being analyzed for oil. Recent postings (May 18, 23 and 25) by BP from the R/V Brooks McCall that is carrying scientists from NOAA, EPA, and BP show a fairly consistent 5 ppb background fluorescence with spikes up to and slightly above 20 ppb at 1,200 meters. The background could be attributed to a number of things, including the fact that there are 63 natural seeps in the northern Gulf of Mexico that contribute approximately 20 million gallons of oil annually (click here and here for details). From all appearances, a plume of oil is moving deep below the surface, while oil is also moving on the surface and contaminating the shorelines of Louisiana.

Take Home Lessons from Microbiology

by Mark Martin

I just attended the American Society for Microbiology Conference for Undergraduate Educators in San Diego, along with many other enthusiastic teachers of matters microbiological. At the end of that conference, we heard Amy Cheng Vollmer, 2006 Carski Foundation Distinguished Undergraduate Teaching Award Winner, challenge instructors to finish the statement "It's not what we say..." Personally, I answer "...it's what the students take away from the course."

Mark's Spring 2010 Microbiology class.

What kinds of things stand out to a student about a given class? At my university, I teach the only microbiology course available, a course generally taken by seniors. I asked the following question of my Spring 2010 class: What ONE concept or idea (that you did NOT know coming into this course) do you feel has been most important to this class? Here are some representative responses: