Small Things Considered

What Microbiological Discovery in 2008 Did You Find Especially Interesting?

Here is one answer to our query. We invite you to send us yours to add to this post.

by Ferric Fang

One of the most interesting microbiology papers I read in 2008 is by Isalan et al. These authors found transcriptional regulatory networks in E. coli to be unexpectedly robust in response to perturbations from the construction of novel artificial connections. Most changes were compensated for and had no effect on growth, and some even appeared to enhance fitness. The authors concluded that regulatory networks are highly plastic and evolvable. (See the commentaries by Ideker and by Bennett and Hasty.) And yet, an equally interesting study by Lercher and Pál suggests that newly acquired genes take a very long time to become integrated into existing regulatory circuits over evolutionary time. If regulatory networks are so readily modified, why does the addition of new components take so long?

Giardia: "I Did It My Way"

by Merry

Giardia lamblia trophozoite. This is the
motile, feeding stage of the parasite found
in the intestine of humans and other mammals.
Scanning electron micrograph, false color.
Credit: Joel Mancuso, Univ. of CA, Berkeley.

Even if Giardia lamblia weren't one of the most common human parasites, it would still garner its share of attention. It is one of the earliest diverging eukaryotes, and it has its own way of doing things. For starters, it has two apparently equivalent diploid nuclei, both of which are transcriptionally active. (Why does this matter? Find out below.) Its genome is exceptionally compact, with unusually short intergenic regions and only a handful of possible introns. Where other eukaryotes use multi-domain proteins, Giardia gets by with simpler versions. In common with many parasites, it does without numerous metabolic pathways, relying on a supply of product from its mammalian hosts. It also does without functional mitochondria, making do with mitosomes─mitochondrial relicts that lack a genome but carry out the mitochondrial function of assembling iron-sulfur protein clusters.

During its motile feeding or trophozoite stage, it lives and reproduces in the small intestine of humans and other mammals. It attaches to the intestinal wall by its unique adhesive ventral disc. No receptor sites are involved─it also attaches to the wall of the container when grown in culture. In the small intestine, it has to defend itself not only against the immune system of the host but also against digestion by the abundant proteases and bile. As defense against both, it cloaks its surface with a dense, 18 nm thick layer of protein, even coating its four pairs of flagella.

Fine Reading: The Hybrid Two-Engine System of Myxobacteria

by Merry

Schematic of the type IV pilus machine omitting 7 of
the pilin proteins "for the sake of clarity." Source

Microbiologists have been fascinated by the social swarming of the myxobacteria since they were first isolated by Roland Thaxter in 1892. Traveling in "wolf packs," these bacteria glide along solid surfaces, such as agar. En masse they secrete enough extracellular enzymes to lyse and digest bacteria, the potential prey they meet on the way. A great deal is now known about how the individual cells in the swarm move about. In a recent review, Dale Kaiser covers the topic from one end to the other—in both genetic and molecular detail. But don't let the pages of details deter you. Even if you skim them, you will still enjoy the unfolding story.

In short, Myxococcus xanthus "glides" using two engines, one at each pole of the cell.

Preventing Infections by Dispelling Sphignorance

by Norm Radin

Although sphingolipids have been known for more than 100 years, this class of body components is known by relatively few biological researchers. Shown below is sphingosine, the simplest sphingolipid.

Sphingosine.

The lonely double bond between carbons C-4 and C-5 is very important to living beings; its proximity to the C-3 hydroxyl introduces properties that are responsible for a surprisingly wide range of important biological functions. The string of three carbon atoms (C-3, C-4, and C-5) is called an allyl group because of the double bond; the C-3 hydroxyl is therefore an allylic alcohol. Some sphingolipids lack the double bond; significantly, they also lack the biological effects.

Organic chemists know that the OH in allylic alcohols is pretty easy to remove or displace with some other negatively-charged ion. While the OH is floating off from C-3, the double bond can migrate. Thus, when the OH (or a new anion) settles back in, it sometimes goes to C-5 instead. It can also return to C-3 but on the other side, so the new molecule is a mirror image of the original one. These allylic reactions were not known in the bad old days, giving sphingolipid chemists the feeling that they were dealing with a Sphinx-like group of substances. Thus, their name, misspelled by thousands of secretaries and typesetters as spingolipids (easier to pronounce). Strangely, few pharmaceutical and biological chemists know about the properties of allylic compounds despite their occurrence in many life forms and important clinical drugs. This has given rise to a word for inexplicable ignorance, sphignorance.

Talmudic Question #43

by Mark Martin

How might the botulism bacillus, Clostridium botulinum, benefit from making botulinum toxin? (This question can be extended to the tetanus bacillus and its toxin, as well as to others.)

A Glimpse Into the World of Metagenomics

This commentary was submitted to us in response to our post, Fine Reading: Metagenomics, published on October 16, 2008.

by Donald A. Klein

The article entitled Metagenomics that recently appeared in Nature provides interesting insights into how metagenomicists appear to view microbes and the field of microbial ecology. What are some of the assumptions that are being made, based on the information given in this article?

In the Company of A Microbiology Blogger and Mushroom Hunter

posted by Chris Condayan

Hear Elio speak on the “Meet the Scientist” podcast. He is being interviewed about the joys and uses of microbiology blogs and mushroom hunting by (another Merry) Merry Buckley. The episode is about 16 minutes long.

To listen now, click the play button under the image on the left. If you would like to download the file and put it on your computer or MP3 Player click here. You can subscribe for free to Dr. Merry Buckley's Meet the Scientist podcast via iTunes, through the RSS feed, or by email alert.

Another Ralph Story

by John Ingraham

This one was contributed by John Ingraham, in response to our post about Ralph Lewin (see below).

Heres a Ralph Lewin story you might not know. Ralph and Mike Doudoroff (another polymath: student of butterflies and snakes as well as microbial metabolism and taxonomy) were great friends. At the annual Asilomar meetings, Mike and Ralph always hung out together and interacted to everyone's delight and mild apprehension.

On a Saturday of one of the meetings, which would run till Monday, with smiling Ralph beside him, Mike stood up and announced that he was a bit disappointed with the proceedings: Whereas speakers used to share enthusiastically their latest findings, now they only reported results that had been confirmed, reconfirmed, and accepted for publication. So to rekindle the spirit of the meetings old vitality, he and Ralph wanted to report on an experiment that was still under way.

Of Fly Paper, Esperanto, Algae, Poems, and Polar Bears: In Memory of Ralph Lewin

by Elio

Picture a leading authority on algal genetics and ecology, a discoverer of fascinating microbes from many phyla, an accomplished poet, an Esperantist who translated Winnie the Pooh into that language, a wit, a philosopher, and a nice guy. You have pictured Ralph Lewin, who died in La Jolla, California, in late November. He was one of the last romantic polymaths of science.

In brief celebration of Ralph's contributions, I will recount just one of his discoveries: a novel way evolved by certain bacteria for preying on others. The predators are saprospiras, marine gliding bacteria in the phylum Bacteroidetes. They make long, multicellular, helical filaments that glide on solid substrates at the goodly rate of 2-5 μm/second, presumably the result of streams of extruded surface mucilage. Abundant on marine sand, they subsist, in part, by killing other bacteria and protists, then digesting their constituents. How they grab their prey is what's so unusual here.

Wolbachia Infection: A Good Thing?

by Merry

Drosophila melanogaster.
Source

Wolbachia have caused one of the great pandemics in the history of life. They infect at least 20% of the species of arthropods—which adds up to about 10⁶ species—as well as other invertebrate hosts. And they have done this using only maternal (vertical) transmission to infect their next host. Maternal transmission is an imperfect mechanism because all of the progeny eggs don't become infected. If this were the only factor, the percentage of Wolbachia-infected hosts would decrease with each generation. In the course of time, the symbiont would be eliminated from the population. Since the Wolbachia are still here, some other factors must be at work.