Small Things Considered

Short Courses for Long-Term Learning

by Phoebe Lostroh

A view of Colorado Springs, the home of Colorado College, where the author teaches.

Good microbiologists question assumptions. How about the assumption that semesters are the best calendars for learning? What would happen if rather than taking four courses concurrently during a semester, students instead took those four courses successively, one at a time? This describes the Colorado College “block plan,” first implemented in 1970. We teach every undergraduate course, from Arabic to Zoology in periods of 3.5 weeks.

You may wonder how such a calendar works for science courses with laboratory or field components. But in fact, microbiologists already believe in this model of immersive science education. Consider the short courses offered at the Marine Biological Laboratories, or Cold Spring Harbor. These, however, are courses for advanced students. Would undergraduates learn anything in such a small period of time? The fact that Colorado College graduates go to medical and graduate schools at the same high rate as that of most liberal arts college graduates suggests that they learn their lessons well. And sadly, there is all too much evidence that students learn precious little in most undergraduate science courses. Why not try something different?

Pictures Considered #1. Visualizing Coupled Transcription and Translation in E. coli

by Elio

Some images that have appeared in the literature from time to time are truly iconic in that they tell the underlying story clearly and succinctly. We present here images that have made a difference in microbiology at the time. You are invited to suggest your choice.

Visualizing Coupled Transcription and Translation in E. coli

A portion of an E. coli chromosome being transcribed (left to right) and being simultaneously translated. The arrow points to the putative site where RNA polymerase is first bound to the DNA. The chains of dark bodies are polysomes, that is, several ribosomes on the same mRNA molecule. Note that the size of the polysomes increases with distance from the upstream site where transcription began.

In 1970, before this image was published, there was indirect evidence that translation in bacteria is coupled to transcription—a pronounced departure from the eukaryote way in which one process takes place in the nucleus while, the other is relegated to the cytoplasm. This classic electron micrograph by Miller, Hamkalo, and Thomas nailed down that supposition beautifully. In the decades since, this has proven to be one of the few enduring criteria for differentiating between prokaryotes and eukaryotes.

 

A Passing Thought

by Elio

Sections of Rockyard Chalcedony (var. Agate) from Burns, OR. Except for the colors, might a section through feces look like this? Source.

In the celebrated novel The Rebel Angels, the famed Canadian author Robertson Davies mentions Ozias Froats, a fictional professor potentially on his way to a Nobel Prize for discovering that everyone’s feces reflect the maker’s personality. He did not have today’s ready recourse to metagenomics (that being still in the future), so he looked at "extremely thin slices of faeces, cut transversely, and examined microscopically and under special light.” He found that each person’s specimen reveals differences in individual temperament. It occurred to me that using this same approach could add another dimension to fecal metagenomics by determining the intra-turd location of individual species. This could readily be visualized using specific fluorescent-labeled antibodies on thin sections—merely a technical elaboration on Froats’ methods.

I know little about how feces are made (“turdopoiesis”) except that it involves dehydration of the colonic contents. In the process, some bacteria are surely displaced mechanically but others perhaps turn on their motility apparatus early in the process to travel to a preferred site, be it the edge or the interior of the creation. Do those species that cling to the mucosal surface or inhabit the mucus also get carried along? Or are they found mainly on the surface of the bolus? And what about prophages, which may well come to life as the result of bacterial stress? Sampling for metagenomics is easier to do with feces than with the insides of the gut, but at present we know little about the geometry of microbe-rich environments and their dynamics.

Froats saw much beauty in his work. He described what he saw in the sections as "splendid cuttings of moss-agate, brecciated agate, an extraordinary beauty reminiscent of ‘that chalcedony which John's Revelation tells us is part of the foundations of the Holy City’." Who knew? Anyhow, with individualized medicine upon us, perhaps standard laboratory tests in the future may include cutting sections of fecal samples for microscopic evaluation. Besides, this may give the person doing the examining unexpected visual pleasures.

Book Review: Viruses: Essential Agents of Life

by Welkin Johnson

Virology was born in 1898, and has suffered from sampling bias ever since. For decades, viruses were defined by what they were not: not as big as a bacterium, not visible with a microscope, not culturable in the absence of a host. At the dawn of the 20th century, undiscovered viruses and aspiring Hollywood starlets had the same challenge—how to catch someone’s attention. Thus, the first viruses known to science were those causing very obvious phenotypes in clinically or agriculturally important hosts: yellow fever in humans, mosaic disease in tobacco, foot-and-mouth disease in livestock. The acid-test was the ability to pass through the pores of a Chamberland or Berkefeld filter; the viruses that were easiest to find were those that produce infectious cell-free virions—another source of discovery bias. And, in the days before cell culture, the easiest of those to study were the ones that induced rapid and obvious pathogenesis in a conveniently available host organism. By mid-20th century, technology fostered the move to reductionist experimentation, including electron microscopy, X-ray crystallography, cell-culture and, of course, recombinant DNA technology. Virologists moved into laboratories, and the model systems they chose to bring with them were often those already in place, proven to be tractable and considered relevant by funding agencies. Today you can peruse any virology textbook and get the impression that less than two dozen viruses represent the entirety of Earth’s virosphere.

Teaching Students To See Through “Microbial Eyes"

by Mark O. Martin

The voyage of discovery is not in seeking new landscapes but in having new eyes. - Marcel Proust

At my primarily undergraduate institution (3,000 students total, 12 Biology faculty, over 50 Biology majors graduated per year), there is only one microbiology course, and it is generally taught to seniors (and not all seniors at that).  Considering the power and primacy of the microbial world, I have always found that lack of coverage pedagogically unsettling.  No biology major could graduate without learning a fair amount about plants; what about bacteria and archaea?  It is certainly true that some classes—cell biology, genetics, and molecular biology come to mind—have aspects that intersect with matters microbial.  But I find that my seniors, after a semester of my prokaryotic proselytizing, are very aware of a significant gap in their education.

“Doc Martin’s” 2012 Microbiology class.

This is why I would urge any and all microbiologists out there to push for more microbiology, earlier in the curriculum, both in lecture and laboratory.  I do what I can to promote “microbial pride” among my seniors, as you can see from the photograph of my class this semester.  I even came up with a logo, which I showed during a presentation at the American Society for Microbiology General Meeting in San Francisco last June, suggesting that we microbiologists should push to “occupy the curriculum,” intellectually speaking. After all, consider how genetics, molecular biology, and biochemistry have progressed over the past century.  Now consider the path of that progress without the use of prokaryotes as a model system!  I believe we will also find that the fields of ecology and evolution will also be equally as indebted to bacteria and archaea over time.

Book Review: Son of Double Helix

The Annotated and Illustrated Double Helix. By James Watson. Edited by A. Gann and J. Witkowski. Simon and Schuster, 2012.

by Elio

This reissuing of The Double Helix, now adorned with umpteen photographs, reprints of first pages of articles, personal letters (some in scrawled—illegible—handwriting), sketches, etc., is not your usual reprint, but I hasten to say that it does make sense. The added material fleshes out the events of that time, with collected accouterments that appeal to both the eye and the mind. Some are purely illustrative (e. g., a photo of the Idlewild Airport observation deck in the late 1940s or a heavy foggy November night in London in the 1950s) and could be considered superfluous, but most are OK, or even better than that.

Despite later claiming that they had thrown out many early documents, the key participants in the early days of research on the structure of DNA had obvious pack rat tendencies as they saved a lot of now precious stuff ranging from letters to doodles on napkins. And a good thing that is. These informal documents often provide us insights into the turbulent goings on of those days—events that appeared especially turbulent when reading Watson’s original 1968 edition. Do you wonder what really went on? Did W&C embezzle Rosalind Franklin’s X-ray image? Did they make sure that she did not get proper credit? Did their Nobel-prize fixation lead to inappropriate actions? The details assembled here provide clues for the merely curious and the absorbed scholar alike.

Why Medical Microbiology Is Not Like Stamp Collecting

by Elio

Wonder, at the 2010 Edinburgh International Science Festival. Image credit: Edinburgh Festival Guide. Source.

I started teaching microbiology to medical students in 1958, at a time when biomedical science was in its full ascendancy. Grant money was there practically for the asking, jobs were plentiful, universities and their medical schools were frenetically building up their science base. Not entirely surprising, the general feeling of young Ph.D.’s such as myself in basic sciences departments was that we were doing the medical students a favor by stooping to teach them. Maybe I exaggerate, but not by much. We had a long ways to go.

Art on a Dish

by Elio

Fleming was one of the first to explore microbial art by creating “germ paintings” using living bacteria. Source.

Quite a few years ago, I spent some time viewing a natural history-inspired show at the Boston Museum of Fine Arts. One exhibit that especially caught my attention consisted of a meter-square dish containing what must have been EMB agar. This “plate” had been left exposed to the air and the ensuing mold colonies were allowed to grow until they became confluent. The result was stunning: individual molds displayed their natural colors plus those of the dyes (methylene blue and eosin) they selectively picked from the medium. The result was a riotous jumble of exceptionally vivid colors, from blues to reds.

Darwin, as portrayed on agar using E. coli, by students in the Gregory lab. Source.

Although such “microbial art” is impermanent, it has had its adherents since the early days of agar plates. In fact, Alexander Fleming “drew” portraits, and even a pair of phage particles fighting. He inoculated the plates using pigmented bacteria and incubated the plates until growth became evident. To quote from this website Apparently he prepared a small exhibit of bacterial art for a royal visit to St Mary’s by Queen Mary. The Queen was ‘not amused and hurried past it’ even though it included a patriotic rendition of the Union Jack in bacteria.

Fungal Meningitis Bulletin

by Elio

Exserohilum rostratum conidia. Source: AP Photo/CDC

We seldom post items of immediacy, but here we interrupt our leisurely ways to write about the current disastrous meningitis outbreak caused by the injection of fungus-contaminated steroids and other drugs. As microbiologists, the question comes to mind at once: Who is the pathogen? The fungus implicated is Exserohilum rostratum (although a couple of cases were due to the more familiar Aspergillus fumigatus and to a Cladosporium). Like many good fungi, E. rostratum has a couple of synonyms: Setosphaeria rostrata and Helminthosporium rostratum. If you never heard of them, you’re in good company. Neither had an expert on fungal infections who I asked, nor had I despite occasional dealings with fungi. The reason is that there are lots of species of such molds, many of which cause exceedingly rare human diseases.

E. rostratum is one of the dematiaceous or darkly pigmented molds that is found in soil, on plants and in stagnant water. Like many molds, it can be identified under the microscope by the morphology of its conidia (asexual spores), which are quite distinctive. The rare human infections it causes are typically of external body sites, e.g., the skin, cornea. Being common in the environment, it is likely that it contaminated the injectable medications before they were packaged.

A Lovely Event

by Elio

The American Society for Microbiology has designated the Cold Spring Harbor Laboratories on New York’s Long Island as a Milestone in Microbiology site. This is the ASM’s way of recognizing locations where important microbiological history was made. For previous sites so honored click here. Cold Spring Harbor has in fact been called the Mecca for molecular biology (read molecular microbiology, as initially the two were one and the same) and here's why. For a short video of the dedication ceremony, click here.

The Cold Spring Harbor Laboratories seen from the cove. Source.

The early days of molecular biology, say from the late 1940s until about 1965, had a magic quality that seems almost quaint now. The founders of this science were extraordinarily communicative and collegial. True, this was a time when abundant low-hanging fruits were ripe for the picking, plenty for all comers. But personal interests counted for little. Everybody told everybody else what they were doing, and as soon as possible. These being pre-internet days, they devised a new means of communication, the “preprint.” People habitually mimeographed (this being before copying machines) their papers at the same time they submitted them to a journal, and sent around copies for all to read.