Small Things Considered

Mining the Proteome

by Merry

If you had oodles of proteomes at your disposal, what sorts of questions might you ask? A group of Polish investigators classified the proteins in 1784 (!) proteomes based on their isoelectric point and found some interesting correlations between the isoelectric point (pI) of the individual proteins and their length.

Calling All Teachers

As the school year begins, we would like to hear from you about uses that you may have for this blog in your classroom. We think that the material here lends itself particularly well to use as supplemental readings─providing intellectual enrichment to students who desire it. The blog has been mentioned in class syllabi, usually under "Further reading" or "Interesting material" or some such heading. And indeed, this accurately depicts one of its uses.

But we would like to encourage you to consider various other uses, as well. We know of several more active ways in which the blog has been utilized already.

Rearranging the Furniture

Now that nearly a hundred posts reside in our archives, it is high time to reassign them to new categories─categories based on the topic considered. Look at the new list displayed in the right-hand column of the blog. Because of the nature of the material, quite a few items are cross-listed in several categories.

Please let us know if this works for you and let us have your suggestions on how to improve either this blog’s content or layout.

E. coli in Good Spirits

by Merry

Scanning electron micrograph of E. coli,
grown in culture and adhered to a cover
slip. Credit: Rocky Mountain Laboratories,
NIAID, NIH

There is something both endearing and enduring about E. coli. Just when you think that all kinds of other fascinating bugs are about to give it a shove into history, news emerges of its renewed importance. This time, it's biofuels.

Visiting Rome, Dried Figs, and Streptomycetes

Mosaic from Herculaneum
showing various foods du jour.

One of our favorite microbiological blogs (Twistedbacteria) is devoted to the actinomycetes. A July 12 post called Rome, Dried Figs, and Streptomycetes highlights an article purporting that dried figs from Herculaneum were a health food for the inhabitants─a source of antibiotics.

A Bacterial Mouth

by Mark Martin, guest author

I have really been enjoying reading this blog over the past few months. Not only is this type of blog of interest to students and microbiological mavens, but the articles and the comments sometimes bring up prokaryotic nuggets not easily found in the literature! Thus, I appreciate the opportunity that Elio and Merry have extended to me, to tell a weird and wonderful microbiological tale.

This tale begins with Elio's Talmudic Question #3: Why are no bacterial pathogens known to use a Bdellovibrio-type of mechanism to penetrate into eukaryotic cells? Since I have done a little work with predatory prokaryotes, this subject particularly interests me. We are only now starting to understand how Bdellovibrio obtains entry into that enigmatic compartment of Gram-negative cells, the periplasm. Type IV pili have been implicated by a recent publication from Liz Sockett's group in the UK. The periplasm is quite a unique place (see this recommended book by Ehrmann), full of osmotic challenges and diverse solutes, with a gel-like consistency. (At an ASM meeting many years ago, Terry Beveridge of the University of Guelph of once chided me for saying "periplasmic space" instead of "periplasm" for that very reason.)

Eukaryotic cells do not possess a periplasm, so the simplest way to answer Elio's question may be to state that there is no need for a Bdellovibrio-like mechanism. Instead, pathogens and symbionts hijack the mechanisms that eukaryotic cells use to internalize materials from their surroundings: phagocytosis and pinocytosis. So I would turn Elio's question around with a not-quite Talmudic reply: why do prokaryotes not have phagocytosis or pinocytosis? This lead us to a seemingly bizarre question: can a bacterium have a "mouth"?

Electron micrographs of Sphingomonas strain A1 in the absence (left) and
presence (right) of alginate. Source: See below.

Sprezzatura in the Lab

Sprezzatura is a term from the Italian Renaissance that denotes the art of making the difficult look easy, a kind of non-chalance. Examples are the Mona Lisa or Michael Jordan at work. In science, some extraordinarily difficult experiments are made to look easy when described in a paper. But we are not so easily fooled; we know what went into them.

I have two recent examples in mind.

Microbial Endocrinology: A Coming of Age

Stress. Source: Univ of
Northampton Mental
Health Postcards

If you stick around long enough, you recognize a rhythm in science as old motifs resurface every now and then, gain prominence for a while, and then fade away. In my mind, tantalizing examples from the tides of Medical Microbiology include the elusive role of microbes in chronic diseases, the indications of long-term perseverance of pathogens in the body, and the persistence of bacteria following exposure to antibiotics. Surely readers with bifocals can add to this list.

Yet another recurrent topic is the relationship between infection and hormones, recently termed Microbial Endocrinology. (For a review on this subject, click here.)

A New Photosynthetic Player

A recent article in Science describes the identification of a novel photosynthetic bacterium in springs in Yellowstone Park. Its presence within the phototrophic microbial mats was detected by metagenomic analysis. This bacterium does not belong to any of the five phyla previously known to have chlorophyll-driven photosynthetic ability (Cyanobacteria, Chlorobi, Proteobacteria, Chloroflexi, and Firmicutes) but belongs to the Acidobacteria.

Amaya Garcia, a member of the research
team, next to Octopus Spring. Photograph
by David Strong. Source: Penn State Dept.
of Public Information

Adding a new and interesting phylum sounds important all right, but still we wondered about the deeper meaning of the finding.  Not being experts in this area, we asked soil microbiologist David Lipson. His reply:

Acidobacteria make up at least half of the sequences found in most soils, very few have been cultured, and those that have so far were all organotrophs.  This shows that they are possibly as physiologically diverse as they are genetically diverse!

Plants and Animals Converse with Microbes in the Same Language

We've eavesdropped before (here and here) on the intimate chemical conversations between pathogens and their invaded hosts. Some plant-bacterium interactions are especially well known, such as those between plants and crown-gall bacteria or nitrogen-fixing rhizobia. What escaped our attention was that the mechanisms used to recognize the invaders can be similar in plants and animals. Both groups take note of the presence of commonplace microbial molecules. (A persnickety aside: one term often used for these microbial components is PAMPs─Pathogen-Associated Molecular Patterns. Because these constituents are found in pathogens and non-pathogens alike, some of us much prefer the term MAMPs─Microbe-Associated Molecular Patterns). MAMPs include components of the bacterial cell envelope, bacterial flagella, and virus-associated nucleic acids. They are, in Lewis Thomas's words, the microbes' visiting cards.