Small Things Considered

Plasmalogens Have Evolved Twice

by Howard Goldfine

Some biologists go blissfully through life without paying much attention to lipids. They do this at their own risk, because there are innumerable things to be learned from their study, including, as we will see here, many relevant to the understanding of evolution. Lipids come in unexpected and exciting varieties, a point that has been acknowledged in this blog (for examples, see here and here)

The lipids that make up the membranes of prokaryotes are polar, that is, they have a moiety such as phosphate, linked to one of the carbons of their glycerol backbone (non-polar triglycerides are generally not known to be made by prokaryotes). The lipids of aerobic and facultative bacteria are mainly of the phospholipid or glycolipid type, in which the first two carbons of the glycerol backbone are linked to long-chain fatty acid esters (Figure). The situation, however, is different in many anaerobes, including both Gram-positive and Gram-negative species, in which the membranes contain both diacyl lipids and compounds known as plasmalogens, in which the chain linked to the first carbon of the glycerol is attached through an O-alk-1’-enyl ether bond (Figure) rather than an ester bond. Plasmalogens were accidentally discovered by Robert Feulgen in 1924. He observed that the cytosol of animal cells turned red when stained with a colorless fuchsin-sulfurous acid reagent, aka known as the Schiff reagent. Such staining reveals compounds that contain aldehyde groups. The red color did not appear if Feulgen’s preparations were first treated with alcohol. He called these compounds plasmalogens meaning “aldehyde-forming substances found in the plasma.” It wasn’t until the 1950s that the correct structure of these ether lipids was worked out. Feulgen and others found plasmalogens in many animal tissues; they are present in especially high concentrations in the brain, CNS, and muscles. Indeed, >60% of the phosphatidylethanolamine (PtdEtn) of our brain is in the plasmalogen form.

Biofilms Over Troubled Waters

by Mark O. Martin

Source.

The old saying “pouring oil on troubled waters” is a metaphor for bringing peace to a turbulent situation. Recent events in the Gulf of Mexico have proved the contrary, that oil poured (or spilled) upon seawater can produce the very antithesis of calm. After many weeks of concern, and with the long term threat of possible subsurface oil still strong, recent reports note that the oil slicks at the surface have become more difficult to find. What is happening? To be sure, dispersal over time is inevitable, but there may be more to the “vanishing” oil slicks.

What we perceive as the leakage of a toxic fuel into the ocean might be seen as an aliphatic feast by marine microbes. Quite a bit of literature describes the relationship that microbes have with oil (for a review, click here) and the possible role for such microbes in bioremediation of oil spills.

Burning off slicks. Source.

Researchers who investigated the aftermath of prior oil spills found that microbes can be involved in the amelioration of such accidents, acting as natural bioremediation agents, as we'd expect on Planet Microbe. Alkane-degrading microbes can in fact increase in population in response to petroleum contamination, as observed in studies ranging from Antarctica to Spain. However, such studies tend to focus on the impact of oil on shorelines instead of on the ocean surface itself. As I watched televised coverage of the spreading oil slicks in the Gulf, I recalled a short paper I had assigned to my latest microbiology class, which suggested that the very surface of the ocean itself could be thought of as an enormous, but very thin, biofilm. This short review by Cunliffe and Murrell credits the biological oceanographer John McN Sieburth with visualizing the air-sea interface as a gelatinous microlayer—a huge biofilm that may cover 70% of the Earth’s surface! (Click here to listen to an interview with Michael Cunliffe.)

When the End Is the Story

by Welkin Johnson

It looks like a herpesvirus, but does it replicate like one?
Electronmicrographs showing mature HHV-6 particles
emerging from an infected cell. Source.

Sometimes, discovery in biology is about discerning rules and sometimes it is about pursuing exceptions. In this spirit, Human Herpesvirus six (HHV-6), the etiologic agent of the common childhood illness roseola infantum, is shaping up to be an intriguing exception. As every virologist knows, members of the Herpesviridae maintain their large double-stranded DNA genomes (typically 100-250kb) as autonomous, covalently closed circles (episomes) during latent infection of host tissues. Nevertheless, there is now convincing evidence that the HHV-6 genome can, at least on occasion, become integrated into host-cell chromosomes. Interestingly, the first hints that this could happen did not come from hypothesis-driven laboratory experiments, but from a handful of clinical case reports of individuals with exceptionally high levels of HHV-6 DNA in peripheral blood.

HHV-6 was discovered in 1986, and its sibling, HHV-7, in 1989. In 1988, a link between HHV-6 and roseola infantum was established. Together HHV-6 and HHV-7 are now categorized as Roseoloviruses, constituting their own genus within the family Herpesviridae. As with the other human herpesviruses, HHV-6 and HHV-7 infections are widespread among humans, but are generally not associated with severe pathogenesis except under conditions such as acquired or induced immunodeficiency. Of the eight known human herpesviruses (officially referred to as HHV-1 through HHV-8), most of us have heard of the Herpes simplex viruses (HHV-1 and HHV-2), the agents behind cold sores and genital sores, respectively, and we are familiar with Varicella Zoster virus (HHV-3), the cause of chickenpox, and Epstein-Barr virus (HHV-4), the cause of “kissing-disease” (infectious mononucleosis).

Fine Reading: The Sex Habits of Fungi

by Elio

Schizophyllum commune. Source.

As luck would have it, two pieces of writing on the sex habits of fungi appeared within days of each other. One is light reading, a post in the admirable Cornell Mushroom Blog entitled A Fungus Walks Into a Singles Bar. This is a précis into the complex story of fungal sexuality. It takes you friendly fashion through the maze of mating types and multiple “genders.” One mushroom, Schizophyllum commune, has more than ten thousand of them! (I once proposed sitting around and making up names for at least a few dozen of them. Any takers?) While you are there, have a look at some spectacular movies of mushroom development, especially stinkhorns (yes, again).

An Inactive Mine Provides Active Opportunities

Acid mine drainage in Spring Creek down-
stream from the Richmond Mine, part of
the Iron Mountain Mine Superfund Site
nine miles northwest of Redding, Calif.
Microbes inside the mine eat pyrite─fool's
gold─to produce sulfuric acid, creating the
most acidic groundwater ever measured.
Spring Creek flows eventually into the
Sacramento River. (UC─Berkeley) Source.

by Elio

“...a riddle, wrapped in a mystery,
inside an enigma...”
                                  Winston Churchill

Metagenomics is a fine tool indeed for surveying a microbial community in concert, treating both the cultured and uncultured equally. When the sample studied is rich in microbial variety, as often is the case, the pieces of genomes can be reluctant to reveal the genetic heritage of whole microbes. But there are a few particular environments that are dominated by a handful of species at most, and here this approach allows the reconstruction of complete genomes. That is the case with the acid mine drainage from mineral or coal mines. When mining ceases, all hell can break loose (anthropocentrically speaking). Microbes oxidize sulfides such as pyrite (iron sulfide) into sulfuric acid, which in turn solubilizes iron, copper, arsenic, silver, gold, and other heavy metals. Water no longer being pumped from the mine, this gemish of minerals emerges from seeps and other openings to become a highly toxic, low pH stream that eventually pollutes larger bodies of water. But for some bacteria and archaea, this is a juicy place to live and thrive.