Small Things Considered

Talmudic Question #67

Richard Feynman, the famous physicist, said: It is very easy to answer many of these fundamental biological questions; you just look at the thing! To take him up on it, imagine a microscope that lets you observe single molecules in a living cell at one Angström resolution. What's the first thing you would do with it?

The Twist in the Story

by Kevin D. Young

I'm finally waking up, a twist in my story...
                                                Secondhand Serenade

Source.

My grandmother took a lot of pills. Each week she arranged them in little piles that she dropped into the compartments of a multi-well device, a way to be sure she took each group on the right day and at the right time. The neat thing (to a kid) was their range of colors and shapes–round ones, ovals, squares, triangles and even hot dog shapes, of every primary color and several pastels. Simply magical. But, of course, appearances were irrelevant. Pill size, shape, and color were dictated by medical tradition and marketing; none of these overt characteristics had any impact on their medicinal value. Efficacy was dictated solely by the nature of the compounds embedded in each lozenge.

A handsome helical Helicobacter
pylori. Source.

A similar situation exists for bacteria. They, too, come in a range of sizes and shapes (though not colors when viewed individually, more’s the pity), and for decades these overt characteristics have been used to differentiate these organisms. However, with only slight hints to the contrary, morphology has not been thought to be medically important. Instead, as with my grandmother’s pills, a bacterium’s pathogenicity has been attributed solely to specific virulence factors embedded in these odd packages. This view is beginning to change.

That earlier hint that cell shape might aid pathogenesis? Uropathogenic E. coli grow as filamentous cells during one stage of bladder infection, and these forms were proposed (click here and here) to promote dissemination as the bacterium moved from one host cell to another. However, this was not an airtight conclusion because E. coli also filaments in response to DNA damage, and bladder cells may inflict just such damage to impede bacterial growth. Thus, the observed morphological change might be only a secondary phenotype rather than a primary virulence factor. Along this same line, but in a different domain entirely, cell size of the fungal pathogen Cryptococcus neoformans has also been implicated as a virulence factor. Here, though, the increase in diameter of individual cells from 5-10 µm to 100 µm keeps them from being phagocytized. Thus, the shear bulk of this particular change may be more important than morphology per se.

Trees─Phylogenetic and Real

This is the third post for this year's Week of the Fungi on STC, a sporadic undertaking. This annual festival is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

by Elio

Cyttaria darwinii in Patagonia. Courtesy of Janet Fraser.

Picture yourself walking in a woods where the branches of the trees are festooned with bouquets of yellow objects that on close inspection look a bit like golf balls, dimples and all. This is what you would come across in the beech forests of the southern hemisphere. The yellow balls are fruiting bodies of members of the genus Cyttaria, ascomycetes just like baker’s yeast and morel mushrooms. Cyttarias are plentiful. When mature, they fall off their branches, making a layer up to 15 cm deep on the forest floor. Hard to miss.

Beech Trees, Lake Hauroko, New Zealand. Source.

Cyttarias caught the attention of Charles Darwin during his visit to Tierra el Fuego. He noted that the natives, the Yaganes, ate these mushrooms, although oddly they bypassed fresh specimens in favor of older, wizened ones. Some years ago, I came up with a possible explanation. Uniquely among mushrooms, Cyttaria have a concentration of fermentable sugars. Indeed, in Chile some people use them for the production of an alcoholic beverage called “chicha de llau-llau.” So, could it be that the natives of Tierra del Fuego favored the older specimens undergoing fermentation? These people were surprisingly hardy; they were very scantily dressed, yet living under very harsh climatic conditions. I posited that a little alcohol from fermented cyttarias may have gone a long ways towards good cheer (Ref. 1). Nobody has come up with a better idea.

Color Me Aphid

This is the second post for this year's Week of the Fungi on STC, a sporadic undertaking. This annual festival is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

by Elio

Is it OK with you if on Fungus Week we post an item that deals with fungal genes instead of whole fungi? We want to do this because of a startling finding, that some aphids are colored because they possess fungus-derived genes for making carotenoids. This is news because until now it was thought that animals cannot synthesize such pigments—only prokaryotes, fungi and plants can (which is why vitamin A—a carotenoid—is a vitamin). But there you have it, some aphids are green and others are reddish depending on which carotenoids they make. It had been thought that these animals get their carotenoids either from their diet or from bacterial endosymbionts. However the sap they live on has no such things, and their symbionts lack the genes for carotenoid biosynthesis. In addition, curing the insects of the symbionts does not affect the color. Lastly, the symbionts are inherited maternally, whereas color follows Mendelian inheritance.

        Coloration of pea aphids. (A) typical green; (B) typical red; (C) a green mutant that arose
        from a red clone. Source.

Of course color matters. Animals use color to respond to enemies, find food, and in some cases, seek out a mate. The predators of the aphids are good at telling colors. Lady beetles find red aphids to their liking, whereas certain wasps prefer green ones. And who knows in how many other ways color makes a difference to these insects!

Riding the Spore Wind

This is the third annual Week of the Fungi on STC, a sporadic undertaking. It is our way to hail the start of the fall mushroom collecting season in parts of our home territory (the northern hemisphere).

by Elio

Making a spore print of Agrocybe dura (Basidiomycota),
showing brown spores. Source.

Sooner or later, but usually sooner, anyone dealing with fungi will have to deal with the issue of spore dispersal. Many fungi, mushrooms included, are a spore’s way of spreading spores through the environment. They do this in varied and universally ingenious ways. Spores, like mammalian sperm, are made in excess, which enhances the chances of some “making it.” Anybody who has made the spore print from a mushroom can attest to the large number of spores produced. This is true not only for the Basidiomycetes, to which most mushrooms belong, but also for the larger Ascomycetes, (the group that includes not only yeast but also most molds, as well as larger organisms such as the cup fungi).

For dispersal to be efficient, the spores must travel a certain distance from their place of origin. They are ejected with great force, sometimes challenging our belief. (For a previous article in this blog, click here.) For example, the spores of the ascomycete plant pathogen Sclerotinia sclerotiorum are ejected at a speed of 8 meters/second, but decelerate after traveling only 3 mm. Thus, no matter how forcibly they are popped out, pretty soon they come to a halt because they are small enough to feel the drag from the air through which they travel.

(Left) Section through a gill of a mushroom (Basidiomycota) showing spores (brown, ~10 µm long) ready to pop. Source.

Of Terms in Biology: Monophyletic, Paraphyletic...

by Psi Wavefunction

Reading phylogenies is a skill that can appear deceptively simple at first glance. In essence, it really is simple, but also counterintuitive to the way the mind is used to working. Far too often—and popular literature as well as science journalism is notorious for this—mistakes are made, mistakes as simple as assigning a significance to the linear order of taxa, assuming that the rightmost taxon is the most derived or the ‘highest.’ Furthermore, some terminology like paraphyletic and polyphyletic may seem confusing at first, given that we typically don’t deal with sets of evolutionarily related items in everyday life.

Imagine you have a tree like the one shown here, where A-E are various related organisms. Termini (A-E), or ‘leaves,’ are typically extant taxa, whereas the internal nodes represent shared ancestors. The first obvious thing you can see is that A and B are more closely related to each other than either is to C. D and E are both equally close to A, B, and C, given that the last common ancestor is between these two groups at node 1. For example, naked mole rats (A) and the big-genomed Amoeba proteus (B) are more closely related to each other than either is to giant tree ferns (C), and each of the three is equidistant to Haloarcula quadrata (D), a strange square archaean. (A common misconception would be to assume that tree ferns are closer to Haloarcula than are mole rats or amoebozoans, i.e., that, in our tree, D is closer to C than it is to B or A.)

Cheap Exports

by Daniel Smith

Cheap Exports. Source.

Evolution is often thought of in functional terms. Mutations that improve or diversify a protein’s function are selected for, whereas disruptive mutations are selected against. However, economy can also play a role in protein evolution.

Amino acids used in proteins vary in size, complexity and chemical characteristics, which makes some cheaper to synthesize than others. Consequently, some proteins are more economical to produce than others. Previous studies (click here and here) have shown that abundant proteins are often less expensive to make, thus reducing their cellular cost. However, the connection between a protein's location and its expense has not been appreciated. Recently, the ASM online journal mBio published our paper, Economical Evolution: Microbes Reduce the Synthetic Cost of Extracellular Proteins, which demonstrates that proteins destined for locations outside the cell cost less to produce than intracellular ones.

The Ins & Outs of Those Mysterious Microcompartments

by Alan Derman

Thin sections of the aerobic sulfur bacterium
Halothiobacillus neapolitanus showing aggre-
gation of carboxysomes (arrowhead). Bar =
100 nm. Source.

The planet's most abundant enzyme is also one of its lousiest. It's RuBisCO, the photosynthetic enzyme that mediates the fixation of CO₂ by catalyzing its incorporation into the five carbon ribulose-1,5-bisphosphate (RuBP). Routinely it goofs and incorporates O₂ instead, producing the useless and potentially harmful phosphoglycolate, which cells must then expend energy to dispose of. And even if O₂ is not around to confuse the enzyme, the K_m of cyanobacterial RuBisCO for CO₂ is still greater than 150 μM. The CO₂ concentration in the aquatic environments where cyanobacteria live is typically less than 15 μM. Cyanobacteria and other RuBisCO-containing bacteria deal with ill-behaved RuBisCO by confining it in microcompartments called carboxysomes. Confinement of RuBisCO turns out to be for its own good, and for the good of the cell as well.

Negative stain of purified carboxysomes
isolated from H. neapolitanus. RuBisCO
assemblies are visible inside. Bar = 100 nm.
Source.

The carboxysome is not your typical membrane-bound organelle. No lipids are used in its construction, only proteins, several thousand of them, and mainly of 3 or 4 different types. The 300 MDa icosahedral structure—that's more than 100 times the mass of a ribosome—is 80 to 150 nm in cross section. When first observed in the cyanobacterium Phormidium uncinatum back in 1956, they were mistaken for viruses. In retrospect, those early observers were not that far off. Electron microscopy, taken together with x-ray structures of prominent subunits, suggests that the structural organization of the carboxysome is reminiscent of a viral capsid.