Small Things Considered

Fine Reading: Yet Another Reason to Appreciate Fungi

by Elio

This blog, known as it for taking up the cause of the underdog, was fortified by reading How Fungi Have Shaped Our Understanding of Mammalian Immunology in a recent issue of Cell Host and Microbe. Not only that, but this is an exceptional piece of reviewing. It’s short (a mere three pages), fun to read, and to the point.

So, what’s the case for fungi shaping our understanding of immunology? (Note the inclusion of “mammalian” in the title. A nice departure from the customary anthropocentricity). The author, Gordon Brown of Aberdeen, guides us through both early and late developments, starting with Elie Metchnikoff, the discoverer of phagocytosis who saw yeast cells being engulfed by the water flea Daphnia, through C-type lectins, Toll and Toll-like receptors, and intracellular signal pathways.

Selected seminal discoveries from 1884 to 2006 are shown along with representative images,
including Metchnikoff (1884); zymosan engulfment by PMN (1941); properdin (1954, trimeric
structure); Aspergillus infection in TLR-deficient Drosophila (1996); fungal recognition by
Dectin-1-expressing fibroblasts (2001); collaborative signaling between TLR and CLRs (2003);
ITAM-like motifs and Syk kinase recruitment (2005); the requirement of multiple PRRs for
optimal anti-Candida responses (2006); and enhanced Candida infection in the kidneys of
CARD9^−/− mice (2006). Source.

In the author’s words: …fungi and their components have long been known to influence immune function, and the contributions made from the study of fungal infections are often underappreciated. Well, here’s for trying.

Measuring the Strength and Speed of the Microbial Grappling Hook

by Amber Pollack-Berti

Source.

I’ll admit, I’ve been in love with the type IV pili (T4P) for a long time. After memorizing all those complex pathways for regulation and metabolism, there was something so refreshing and accessible about pili. These bacterial surface appendages are, by their nature, mechanical structures. They are easy to visualize. Their composition is simple: a Type IV pilus is a flexible filament made up of thousands of repeating pilin subunits. Bacteria employ this one structure for a variety of purposes: T4P play structural roles in motility and biofilm formation, and have also been implicated in DNA binding and uptake, in host cell signaling, and even in communication of electrical signals as ‘nanowires’.

T4P are long and thin and have great tensile strength. They are involved in bacterial motility using a special mechanism: the pili are retracted into the cell when the pilin subunits are removed at the pilus’ cell end by an ATPase, the protein PilT. This results in the ratcheting of the pilus back into the cell. When a pilus is attached by its distal end to a surface of agar, the retraction is so strong that the cell is pulled forward in a kind of movement called twitching motility. When a bacterium attaches via the pilus to the surface of a host cell, it retracts until the two come in contact. In these cases, the pilus acts as a grappling hook, pulling the cell along in short bursts of pili elongation, attachment, and retraction.

Fine Reading: Classics from the Archives of the Royal Society

by Elio

The Royal Society announced that it has put 60 of its most memorable papers online. One of them concerns the discovery of bacteria by Antonie van Leeuwenhoek. The original paper as published in the Society’s Philosophical Transactions of 1677-1678 was entitled:

Observations, communicated to the Publisher by Mr. Antony van Leewoenhoeck, in a Dutch Letter of the 9th of Octob. 1676, here English’d: Concerning little Animals by him observed in Rain-Well-Sea- and Snow water; and also in water wherein Pepper had lain infused.

Here are two excerpts that can be expected to tickle the present day microbiologist’s mind. (Note that in the style of the time, the letter “s” looks like an “f.”)

The eye of a body louse is approximately 100 µm in diameter or 10⁴ µm³. The organisms van Leeuwenhoek saw were 1/10 that length, or 10 µm, and 1/1000 that volume, around 10 µm³. Many bacteria reach such dimensions. The movement described matches the runs and tumbles of chemotactic bacteria.

Cryptic Life in the Antarctic Dry Valleys

by Merry

A ventifact (a stone sculpted by wind-driven sand) in
the "Martian" landscape of the McMurdo Dry Valleys.
Source.

On first inspection the habitat seems as sterile as the surface of autoclaved glassware... but the trained eye, aided by a microscope, sees otherwise.
            E.O. Wilson, The Future of Life

For the microbiologist, the next best thing to a trip to Mars might well be an expedition to the McMurdo Dry Valleys of Antarctica. Here, in the Earth's coldest and driest deserts, the conditions approach those on our neighboring planet and are thought to also approach the cold-arid limit for life. Not all of the Dry Valleys are equally dry. Some have perennially frozen, glacier-fed lakes and ephemeral streams, and thus have some soil moisture. Here one finds more of life, even three taxa of multicellular animals—tardigrades, rotifers, and, most numerous, bacterial-feeding nematodes. (Click here for our earlier post about the microbes found in a subglacial lake in this region.)

Lacking such a source of water, thus being one of the truly dry Dry Valleys, is McKelvey Valley. What little snow falls here or blows in sublimates in the cold, hyper-arid conditions. How cold? The average air temperature is around –20 °C. Winter brings prolonged periods of −55 °C cold; in summer, air temperature can rise to a balmy 0°C. Humidity is low (<10% RH in winter). And then there are the ceaseless katabatic winds (from the Greek word katabatikos meaning "going downhill"). Cold, dense air falls downhill off the East Antarctic Ice Sheet and races through the valley at speeds commonly exceeding 50 km/h, sometimes reaching 320 km/h (200 mph). These winds evaporate all moisture and carry sand grains that scour the barren landscape. All in all, these conditions bear some resemblance to those used to freeze-dry biological samples.

Leaf-Cutters Get Their Fix (nitrogen fix, that is)

by Elio

A single leaf-cutter ant fungus garden chamber with the
queen (black arrow). Scale bar: 1 cm. Source.

Ants span a great distance within the human psyche, from being insignificant little nuisances to occupying a prominent place in the biological scheme of things. They surely deserve the latter. Not only do they make up a large proportion of the animal biomass (up to 25% of the total in the tropics), but their social qualities make for substantial mind food. It was not always so. Their very name is tendentious: it is derived from the West Germanic amaitjo, meaning "the biter," from Proto-Germanic ai-, "off, away" + mait- "cut." (If you see little connection between these roots and the word ant, keep in mind the Rules of Etymology, as expressed by a linguist friend: The vowels don't count and the consonants have arbitrary values.)

Few things have the psyche-tickling value of the leaf-cutter ants, those master agronomists that some 50 million years ago learned to cultivate their fungal foodstuff. The leaves they so assiduously bring into their nest become the substrate on which the fungi grow. To deter unwanted fungal species that would otherwise move into their “fungus gardens," the ants harbor bacteria (Pseudonocardia) that make selective antifungal products. But their agricultural endeavors still leave us with a question: Where do the ants get their nitrogen? The plant tissues they use are poor in nitrogenous compounds and, of course, neither they nor their fungi can fix nitrogen. We’ll tell you in a minute, but first a startling digression.

Through the Looking Glass: Silicate in Bacterial Spores

by Peter Setlow

Silicon location in spores. Spores of a high silicate-
adsorbing Bacillus isolate of the B. cereus group
were prepared in silicate-containing medium. TEM
Panel: an ultrathin section of a spore by transmission
electron microscopy. The granules on the outer sur-
face of the coat were absent from spores prepared
in silicate-free medium. (CX = peptidoglycan cortex;
UC = undercoat; CT = coat; SX = silicon-containing
granules; EX = outermost exosporium layer.) SI-K
Panel: STEM-EDX image with the silicon pseudo-
colored green. Merge Panel: TEM and Si-K images
combined. Bar = 100 nm. Source.

Amid the furor surrounding the anthrax attacks in the USA in 2001, significant attention was focused on whether the Bacillus anthracis spores used had been “weaponized” by the adding of a coating of fumed silica to aid in their dispersal. This information might have helped pinpoint where the spores had originated. However, a confusing factor was that for more than 20 years, significant levels of silicon had been reported in spores of at least some Bacillus species, including those of Bacillus cereus, a close relative of B. anthracis. Clearly, the natural presence of silicon in B. anthracis spores makes discrimination between weaponized and non-weaponized spores more difficult. However, in the older reports the silicon was not localized at the outermost surface of the spores, as would be expected if they had been artificially spiked with such compounds.

Anyhow, what is silicon doing on a bacterial spore? A recent paper provides some clues. Starting with soil from a paddy field, these researchers identified a number of novel bacterial isolates that efficiently take up silicate present in media at concentrations comparable to levels found in the water in soils. Strikingly, all of these isolates were Bacillus species and most were members of the B. cereus group that includes the pathogens B. anthracis, B. cereus, and Bacillus thuringiensis. Silicate uptake by the novel isolates was associated only with spore formation (sporulation), and was a late event in this process. However, while sporulation was required for efficient silicate uptake, silicate uptake itself was not essential for sporulation.

An Open Invitation to Argue With Me

by Elio

I have written a “think piece” published in the December 2009 issue of ASM’s journal, Microbe, in which I list my choices of what constitute paradigm shifts in modern microbiology. The choice was entirely idiosyncratic. I am sure that others would include different important developments on their roster. I also make the point that some apparent P.S.’s are really “paradigm drifts. Chacun à son goût, if you pardon my French. So, here’s your chance to expound you views on this matter. What breakthroughs in microbiology do you consider worthy of being called paradigm shifts?

Talmudic Question #57

by Frank Harold

Does anyone know of a solid example of a biological membrane that arises de novo, rather than by the extension of a pre-existing membrane?