Small Things Considered

Bacterial History Found in Ancient Mud Scrolls

by Elio

Dried roll-ups from Bardenas Reales, Spain,
located on a muddy slope close to a vernal
pool. Blade width = 1.5 cm. Source.

Who hasn’t walked along a previously flooded area and seen flakes  of dried mud cakes magically curled up in geometrical shapes? At times, the curls are so pronounced that they make complete scrolls. The area looks like a field of shards. No big deal, just dried mud you might say (as you reach down, tempted to pick up some pieces to play with). Au contraire, such curlicue structures, known as roll-ups, are of considerable interest to geologists. Roll-ups are sedimentary structures capped with a surface layer of clay and organic material that form when the surface dries out. Once formed, they are quite resistant to wetting and weathering, the open curls much less so.

Microbial architecture of a roll-up. Cross-section of a roll-up
from Bardenas Reales, Spain. Layers of cyanobacteria
(increasing in abundance toward the surface) can be seen
intercalated within layers of fine sediment (arrows).
Bar = 0.5 mm. Source.

To explain why we're playing with mud cakes on this blog, it turns out that the roll-ups are largely biogenic. Their surface includes distinct populations of cyanobacteria, which are much less common in the adjacent, non-rolled soil. The cyanobacteria are largely filamentous and of the non-heterocyst forming variety. How do they contribute to the curling? According to H. Beraldi-Campesi and F. Garcia-Pichel of Arizona State, the authors of a recent study, they provide the organic material in the form of bacterial extracellular polysaccharide (EPS). Enough there and it alone can be the reason for the curvature. With less biomass present (<1% of the total), the microbial filaments in combination with their EPS and some fine sediment suffice to do the curling. The authors could reproduce credible roll-up formations by using a clay that swells on watering (smectite) or agar (we hope they enjoyed doing it).

Retrospective, December 2010

This blog is now entering its fifth calendar year, surely a respectable age for a blog, perhaps bordering on the venerable. With the passage of time, our blend of posts has included more and more contributions from guest writers, some from young students, others from experienced and distinguished microbiologists. In other words, this blog has become a bit of a forum where people of different backgrounds and experience can share their excitement for the world of small things. We hope that as this blog enters its next year it will continue to provide you with microbial joys.

As is our tradition, we present here a lightly annotated list that includes most of our posts from the past half year.

False colorized influenza viruses in DCK cells.
Credit: Centers for Disease Control/C. Goldsmith,
J. Katz, and S. Zaki. Source.

Virology

Physical Virology.  Manuel Sanchez tells us how physical measurement can be carried out on a single virus particle, revealing differences in how far a virus can be pushed around. We borrowed this piece from his blog, Curiosidades de la Microbiología.

Tales of Death.  Some Bacteria have turned the burden of viral infection into an opportunity. They have co-opted the elaborate phage tail structures for their own use, for killing specific target Bacteria and, sometimes, even larger game.

 A Giant Among Giants.  Mimivirus made a big splash, but a whole host of giant viruses have been found, mostly in aquatic environments, and more are being discovered all the time. Their genomes carry hundreds of genes, many of them unexpected for a virus.

A Fastidious Bacteriophage.  Michael Yarmolinsky brings back phage Chi from near oblivion. This coliphage attaches to a host's flagellum and then makes its way to the cell surface, taking advantage of the flagellar rotation.

Dr. Rous’s Prize-Winning Chicken.  Welkin Johnson celebrates the 100^th anniversary of Peyton Rous's discovery of an oncogenic virus, now known as the Rous sarcoma virus.

When the End Is the Story.  Welkin Johnson tells us that HHV-6 is unique among human hespesviruses in being integrated into our chromosomes. Not only that, it prefers the telomeres!

Promiscuous Bacteria & Viral Playboys.  Occasionally, phages carry bacterial genes from host to host—one of the mechanisms for horizontal gene transfer between Bacteria. Looking at single bacterial cells, researchers found that genes were delivered more often than we realized, and even to non-hosts.

Talmudic Question #69

by Ramy Aziz

Is there anything microbes cannot do?

A Role for Prions in Alzheimer’s Disease?

by S. Marvin Friedman

Three-dimensional configuration of a prion protein. Left = normal
folding. Right = protein with the disease-associated amyloid
folding. Source.

What if there were a connection between the diseases caused by prions and Alzheimer’s? If that were the case, we'd expect a substantial increase in our understanding of both. Indeed, as we will see below, there is now evidence that the two phenomena are related in some way. But first, a bit about prions.

Mutations at different sites in a normal brain protein, the prion protein (PrP^c), result in misfolded proteins (PrP^sc) that cause a variety of neurodegenerative diseases termed transmissible spongiform encephalopathies (TSE) in both animals and humans. The human diseases include Creutzfeldt-Jakob disease (CJD), while the animal diseases include the infamous “mad cow disease”(bovine spongiform encephalopathy,) and others. The misfolded form of the prion protein acts as a template that leads to the conversion of the normally innocuous prion proteins into infectious, disease-causing ones. Prion diseases are characterized by long incubation periods and “spongiform” changes in the brain leading to neuronal loss. The normal functions of the PrP^c protein are not well understood, although a recent study using knockout mice lacking it suggests a role in the processing of sensory information in the olfactory system.

One in a Million

by Merry

        The genetic code and the amino acids it encodes. Source.

Like it or not, we can't shop around for a genetic code, nor do we have a choice of brand or model. We're pretty much stuck with the one we have at this point (although some researchers are modifying the code to synthesize proteins containing "designer amino acids"). The universal genetic code is just that, virtually universal. Oh, there are about 20 other "genetic codes" known but almost all of them are used only by mitochondria or else the differences are limited to start and stop codons. So how good is the one we have?

Ploidy Redux

Habitat '67 Redux. (Montreal) Photographer: Michael Sirois. Source.

We recently posted a short piece on the term ploidy as it applies (or not) to prokaryotes.  Dana Boyd pointed out that in prokaryotes the term refers to sets of identical chromosomes, unlike in eukaryotes, where each chromosome of a set is usually different. The distinction seems crucial enough to warrant further explication.