Small Things Considered

Has the Time Come? Or Has the Time Gone?

A megaproject. Dubai skyscrapers.
Source: SkyscraperPage Forum

Inevitably, there will be those who believe in the value of high throughput data collection in biology and those who propose that it’s a waste of time and resources. At a time when powerful new methodologies emerge, such extreme views can be expected. The argument is usually about the ultimate value of investing large sums of public money in megaprojects, versus funding individual, hypothesis-driven research programs. A current diatribe concerns the international Protein Structure Initiative, a megaproject aimed at determining the three-dimensional structures of all proteins. A lively debate is taking place in the pages of the journal, Genome Biology. Gregory Petsko, a biochemist at Brandeis, has taken on PSI with a cheerfully-written article with the provocative title An Idea Whose Time Has Gone. Not surprisingly, European proponents of PSI came back with a spirited rejoinder telling us that they think this is “an idea whose time has come.” At the end of their article, there is a rebuttal by Petsko. Point, counterpoint.

We invite readers to come to their own conclusion about which way the arrow points. Conciliatory sorts that we are, perhaps there is a middle ground. At any rate, this is food for thought and highly readable stuff.

Special Interest Symposium

by Elio

At the forthcoming General Meeting of the ASM, which starts Sunday, June 1, in Boston, there will be a Special Interest Symposium on the topic Reflections on the 50th Anniversary of Schaechter, Maaløe, Kjeldgaard. I will report on this on my return.

The Science Social Media Breakfast

Join Elio Schaechter of Small Things Considered and Chris Condayan from the MicrobeWorld Radio and Video podcasts for a lively breakfast discussion about using new media for science communication. All attendees are encouraged to share their experiences in using new media, such as blogs, social networks, video and audio podcasts, and wikis, to promote the life sciences or for use in educational settings.

This event coincides with American Society for Microbiology's 108th General Meeting in Boston, Massachusetts, from Sunday, June 1, to Thursday, June 5, 2008.

Please note that The Science Social Media Breakfast is not directly associated with ASM's General Meeting and is therefore open to anyone in the Boston Metro Area to attend.

For the location and time, and to register, click here.

With a Little Help from Their Friends

by Merry & Elio

EM of phage 80α particles and a SaPI1
particle with a smaller head (arrow).
31,500×. Source

Genomic islands are long stretches of chromosomal DNA that look suspiciously foreign in origin and are found in many pathogenic and non-pathogenic bacteria alike. Some of them, called pathogenicity islands, encode toxins or other factors that contribute to the virulence of the pathogenic ones. It is suspected that they arrived by horizontal transfer, perhaps with the help of a phage. A story has turned up that makes the connection between pathogenicity islands and phages even more plausible.

One in five isolates of Staphylococcus aureus produces TSST-1, a potent superantigen that causes the toxic shock syndrome. The TSST-1 gene is on a mobile pathogenicity island called a SaPI. Such islands are extremely common in this species, with at least one of them found in all but one of the S. aureus genomes sequenced as of 2007. SaPIs share characteristics that set them apart from your run-of-the-mill pathogenicity island.

Fine Reading: Pathogens, Evolution, & Ecology

by Elio

Three Spanish microbiologists (F. Baquero, C. Nombela, and J. A. Gutierrez-Fuentes) plus one American (G. Cassell) edited Evolutionary Biology of Bacterial and Fungal Pathogens (ASM Press, 2007). We needn’t contribute a review of our own because a particularly informative one by Ricardo Guerrero appeared in a recent issue of International Microbiology. This book is most timely because we are becoming increasingly aware that pathogenic microbiology is a branch of ecology. As Julian Davies notes in the Foreword: All microbiology is environmental microbiology and has been for billions of years. This book emphasizes that to successfully ward off pathogens requires an understanding of the evolution and ecology of the interacting partners. How else can we interpret the emergence of new pathogens and the re-emergence of others?

The Blog in the Classroom

by Elio

Students in Integrative Microbiology, a graduate course taught jointly by the University of California at San Diego and the San Diego State University, could fulfill an assignment by optionally answering either one of two specified Talmudic Questions. Their answers are now posted as comments under each of the posts. They make good reading.

Talmudic Question #30. Many bacteria, e.g., E. coli and B. subtilis, regulate their gene expression via a large number of distinct devices that operate on almost all conceivable biochemical levels. Why so many?

Talmudic Question # 6.With the buzz created by the discovery of giant viruses, e.g., Mimivirus, the distinction between viruses and cells is said to get blurred. I maintain that this is not the case because the single most important distinction is that viruses lose their corporeal integrity, cells do not. What do you think? Are you a blurrer or a non-blurrer?

Gulliver and the Lilliputians

by Elio & Merry

"I found my arms and legs were
strongly fastened on each side
to the ground." Gulliver's Travels,
as illustrated by Milo Winter.

Two archaea walk into a bar and the bartender says… No, we don't have an ending for this joke (tell us if you do), but if the temperature of the bar were around 90°C and the locality a hydrothermal vent off Iceland, there is a chance that the pair sauntering in could be one of the most interesting duos around. One partner is Ignococcus hospitalis, an archaeon of respectable dimensions (2μm diameter) that is often seen in close association with the much smaller Nanoarchaeon equitans.

To start with, the names of the organisms were chosen with care. Ignococcus means “fiery coccus;" hospitalis, “host;" equitans, “horse rider.” So, what about them?

Recent Blog Items We've Enjoyed—Spring Harvest

by Elio

Alan Cann’s MicrobiologyBytes has a great video showing magnetotactic bacteria darting back and forth in response to a moving magnetic field.

Besides a lot of other interesting news, Tara Smith’s Aetiology has an update on the case of Robert Farrell, the geneticist who got into trouble for supplying generally harmless bacteria to an artist who used them in an exhibition. The good news is that the case was dismissed (although the Feds can still appeal it).

For the aficionados of Epulopiscium, that Gargantua among bacteria, a new article reports that cells of this fish-gut-dwelling organism are polypoid in the extreme. This gives them some of the advantages of a multicellular organism, a point that Cesar Sanchez discusses (along with some highly pertinent links) in his blog Twisted Bacteria.

In Spanish, Miguel Vicente’s Esos Pequeños Bichitos (Those Small Little Bugs) has a revealing and informative article on Robert Koch and aspects of his private life. Worth polishing up the Spanish you learned in school.

And while you’re brushing up on languages, a blog in French, Le blog des bactéries et de l'évolution deals with the 150th anniversary of the birth of Theodor Escherich, the German physician after whom our best known cellular organism is named. This occasion was also celebrated in 2007 in Nature Reviews Microbiology.

In Evilutionary Biologist, John Dennehy deals with the perennial question: Are viruses alive? We maintain that this should only be asked after a few beers. As a good geneticist, John answered: Living entities are those that evolve via natural selection, and surely viruses should be included in that category. The argument continues, no?

Carl Zimmer’s The Loom talks about his soon-to-appear book: Microcosm: E. coli and the New Science of Life. Having read some of it in draft form, I can heartily applaud this birth.

Fine Reading: Fungal Alchemy Revisited

by Elio

The Chernobyl reactor encased in
cement. It is said that it will remain
radioactive for some 100,000 years.

One of the most breathtaking reports in this blog has been the finding that ionizing radiation stimulates the growth of some fungi, such as those found in the encased Chernobyl reactor. A recent review in FEMS Microbiology Letters expands on this phenomenon and surveys considerably more data. Here you can read about how fungi accumulate some radionuclides and resist powerful jolts of ionizing radiation. You can also learn about their amazing ability to grow their hyphae towards the radiation source and flourish better as the result. In toto, this is an example of the stunning ability of living things to hack it in even the most atrocious of environments. But the point is not just academic. The authors say: Using this recently acquired knowledge, we may be in a better position to suggest the use of fungi in bioremediation of radioactively contaminated sites and cleanup of industrial effluent.

Where Art Thou, O Ribosome?

by Elio

Cryoelectron tomography of a vitrified
cell showing ribosomes and the membrane
(grey) in an optical slice. Ribosomes
determined with high fidelity are green,
those with lesser fidelity are yellow. Source

In a recent post (The Age of Imaging), I mused about advances in microscopy that are revolutionizing our concept of bacterial cell structure. High on the list of amazing developments is cryoelectron tomography (CET), a technique that allows one to look inside bacterial cells. Flash-freezing cells at very low temperatures embeds them in vitreous ice, and this preserves their structures when subsequently subjected to the high vacuum of the electron microscope. This process is minimally invasive and requires no staining. Bacteria frozen in this manner can swim away after thawing! A great tutorial about this technique and its uses is provided on Grant Jensen’s web page.

Cryoelectron tomography has its limitations...