Saturday, August 30, 2014

The Ebola virus disease: classification and naming of a group of zoonotic filoviruses

Are viruses of the Ebola type going to cause the next big human pandemic? So far, the Ebola virus disease, an often fatal illness, has affected local groups of humans, gorillas and other mammals in tropical Africa. Some regional populations of gorillas have disappeared. Ebola viruses are zoonotic: they can move from one species to certain others. For example, humans are susceptible to Ebola, horses are not. Intervals of hiding—times free of infection events—are followed by sudden outbreaks.

Recent news about human-to-human transmission of Ebola viruses in West and Central Africa are alarming. Much about Ebola is not yet understood. Fruit bats of the Pteropodidae family are considered as a key reservoir hosts for the virus, spreading it over long distances. But modern air travel and animal trading can result in outbreaks around the globe at any time. No proven vaccine is yet available [1-4].

Major symptoms of an Ebola infection include abdominal pain, fever, headache, sore throat, nausea, vomiting, loss of appetite, arthralgia (joint pain), myalgia (muscule pain), asthenia (weakness), tachypnea (rapid breathing), conjunctival injection (pink eyes) and diarrhea. Like some other viruses, ebolaviruses suppress the immune system  (see pages 94 and 95 in [1]).

The Ebola virus disease is named after the Ebola River in the Democratic Republic of the Congo (formerly Zaire). In 1976, an Ebola outbreak (Zaire outbreak) occurred in a small Catholic mission hospital in Yambuka, a village in the Bumba Zone district (page 69 in [1]). Today, five species of ebolaviruses are known. They all are named after the area or place at which they were first observed and documented. The following overview is based on the scientifically focused, excellently researched and fascinatingly written thriller Spillover by David Quammen [1].

Zaire ebolavirus (EBOV)
The Zaire ebolavirus is named after the Zaire outbreak mentioned above. The case fatality rate was 88 percent; lower than for untreated rabies cases, but higher than for any other recorded outbreak (see page 71 in [1]).

Sudan ebolavirus (SUDV)
This virus is named after an Ebola disease outbreak in southern Sudan in 1976, causing 151 deaths—a lethality lower than in the Zaire outbreak (see page 76 in [1]).

Reston virus (RESTV)
The Reston virus—probably native to the Philippines—is named after a lab-animal quarantine facility in suburban Reston across the Potomac River from Washington, DC. In 1989, an Ebola outbreak occurred at this facility, known as the Reston Primate Quarantine Unit, among long-tailed macaques (Macaca fascicularis), which were imported from the Philippines for medical research (see pages 77 and 78 in [1]). No illness or death in humans from this species has been reported to date [2].

Taï Forest virus (TAFV)
This virus is named after the Taï Forest National Park in Côte d'Ivoire (Ivory Coast in West Africa), near this country's border with Liberia. In 1992, Christophe Boesch, a Swiss biologist, got infected with Ebola during a necropsy of a dead chimpanzee. Quickly hospitalized and treated in Switzerland, she survived (see page 80 in [1]). 

Bundibugyo virus (BDBV)
The Bundibugyo virus emerged in late 2007 as the fifth ebolavirus species. Twenty people died in a remote mountain region in Uganda. Blood samples flown to the CDC in Atlanta revealed an Ebola-type virus, one that genetically was at least 32 percent different from any of the other four (see page 84 in [1]).

The often-used term “Ebola hemorrhagic fever” (EHF) is a misnomer for Ebola virus disease: many Ebola patients do not show any bleeding at all.

Ebolaviruses, like the Marburg virus, were originally classified as filoviruses (a genus), but are now grouped into the Filoviridae family encompassing the two genera of Ebola-like and Marburg-like viruses.

Keywords: field biology, virology, pathology, taxonomy, terminology, zoonosis, Ebola symptoms.

References and more to learn
[1] David Quamman: Spillover. Animal Infections and the next human pandemic. W. W. Norton & Company, New York and London, 2012.
[2] World Health Organization: Ebola virus disease.
[3] J. H. Kuhn et al.: Proposal for a revised taxonomy of the family Filoviridae: classification, names of taxa and viruses, virus abbreviations. Arch. Virol. 2010, 155 (12), pp. 2083-2103. DOI: 10.1007/s00705-010-0814-x.
[4] Tara's Ebola Site: Ebola Classification and Taxonomy.

Sunday, April 27, 2014

A term in earth science: Great Oxidation Event

The atmosphere of today's Earth contains about 21% of oxygen (O2). Early in its history, the anoxic Hadean Earth—as it is scientifically proposed to have been existed around 4.4 billion years ago—had no interface of life-supporting oxygen. The Great Oxidation Event (GOE), which has been suggested to have occurred at the end of the Paleoproterozoic Era more than two billion years ago, was the time when some amount of free oxygen surfaced into the atmosphere. The appearance of the first atmospheric oxygen molecules was biologically and geologically induced. Then, photosynthetically produced oxygen paved the way for advancing forms of life and triggered the coevolution of the biosphere and the geosphere [1-3]. From the GOE onwards, Earth's atmosphere and oceans became oxygenated over time in stages [4].

The details of how atmospheric oxygen first rose to significant levels remain lost in geologic time. But ideas and answers are found by searching for fossiliferous formations such as ancient sandstone, black chert, black shale and stromatolites. Based on microbial mat fossils and fossil biomolecules, found in such deposits, researchers are looking for clues to understand the photobiochemistry of early organisms and possible routes of oxygen production. For example, fieldwork by Nora Noffke and others has turned up microbially induced sedimentary structures (MISS), including 3.48-billion-year-old MISS—the oldest ever reported [5].

An interesting aspect of this geobiological research is the interdependent, natural occurrence of organic and inorganic chemical processes throughout most of Earth's history. Robert M. Hazen and Dimitri Sverjensky argue that biodiversity and mineral diversity developed closely interlocked after oxygen became available within Earth's near surface environment [1]:
Our  recent chemical modeling suggests that the Great Oxidation Event paved the way for as many as three thousand minerals, all of them species previously unknown in our Solar System. Hundreds of new chemical compounds of uranium, nickel, copper, manganese, and mercury arose only after life learned its oxygen-producing trick. Many of the most beautiful crystal specimens in museums—blue-green copper minerals, purple cobalt species, yellow-orange uranium ores, and others—speak powerfully of a vibrant living world. These newly minted minerals are unlikely to form in an anoxic environment, so life appears to be responsible, directly or indirectly, for most of Earth's forty-five hundred known mineral species. Remarkably, some of these new minerals provided evolving life with new environmental niches and new sources of chemical energy, so life has continuously coevolved with the rocks and minerals.

Snapshots of the intertwined stories of our early home planet are now coming in view, thanks to groundbreaking discoveries. Will those results help us to understand and reconstruct the evolution of other planets and their moons in the solar system and beyond? Was the Great Oxidation Event a singularly Earth-bound affair?

Other terms for the Great Oxidation Event: Great Oxygenation Event, Oxygen Catastrophe, Oxygen Crisis, Oxygen Revolution and Great Oxidation.

Keywords: geophysics; planetary science; solar system; paleontology; mineralogy; paleochemistry; photosynthesis

References and more to explore
[1] Robert M. Hazen: The Story of Earth. The First 4.5 Billion Years, from Stardust to Living Planet. Penguin Books, New York, 2012; see page 180 and others.
[2] Robert M. Hazen: Mineral Evolution [].
[3] Dimitri A. Sverjensky: Mineral Evolution [].
[4] Heinrich D. Holland: The oxygenation of the atmosphere and oceans. Phil. Trans. R. Soc. B 2006, 361. DOI: 10.1098/rstb.2006.1838 [].
[5] Jim Raper: Geobiologist Noffke Reports Sign of Life that Are 3.48 Billion Years Old [].

Thursday, March 20, 2014

Crane nomenclature borrowing from equine nomenclature

Female cranes are known as mares, male cranes are known as roans and the chicks are known as colts [1,2].

Commonly, the term mare is associated with an adult female horse. The term roan refers to a particular color pattern—a mixture of white and color (for example, white or gray sprinkles on a brown coat)—found in animals such as horses and dogs. A horse showing this coat color pattern is called a roan. 

Somehow, these terms made it from the equine into crane terminology. Alex Shoumatoff notes (page 59 in [2]):

For some reason crane nomenclature is borrowed from horse terms. A mother crane is called a mare, the dads are roans. The terminology sounds like it was created out West.

Keywords: biology, ornithology, terminology, male, female.

References and more to explore
[1] Kachemak Crane Watch: SandHill Cranes, August 20, 2008 [].
[2] Alex Shoumatoff: Flight Club. Smithsonian March 2014, 44 (11), pp. 54-67.

Tuesday, March 11, 2014

The three- and four-syllable version of a chemical element name: alumin(i)um

Common ores of the metal aluminum are bauxite and alumina. The English chemist and inventor Sir Humphry Davy christened the metal, which he tried to isolate, after alumina. In 1807, he named the chemical element alumium and then changed the name to aluminum [1,2].  To conform with the “ium” ending of most elements, the name aluminium was adopted in 1812, after an anonymous reviewer objected Davy's naming suggestion in the Quarterly Review. But the reviewer forgot about platinum, molybdenum and tantalum—elements with names that also ended in “um”, like aluminum, without a leading letter “i” [2].

Hugh Aldersey-Williams has more to say about the spelling episode of alumin(i)um [2]:

America and France may have pioneered the development of aluminium, but they disagreed over its spelling. Even the great editor H. L. Mencken is at loss to explain this. In the American Language he is forced to confess: ‘How aluminium, in America, lost its fourth syllable I have been unable to determine, but all American authorities now make it aluminum and all English authorities stick to aluminium.’ Other sources suggest it may have been the doing of Charles Hall. The patents he took out while his commercial publicity material touted the merits of  ‘aluminum’, whether by intent or typographical error is not known. The shorter word spread and stuck in the United States; in France, Britain and the rest of Europe, the extra syllable remained.

The extra syllable was also around in the U.S. until 1925 [1]. Then the American Chemical Society officially decided to use the name aluminum in their publications. Ever since, scientists and engineers are doomed to live with a dual spelling policy for alumin(i)um—switching between aluminum and aluminium depending on which journals they read and where they publish. Fortunately, the element symbol Al is undisputed!

Keywords: chemical element, renaming, history, orthography, typography.

References and more to explore
[1] David R. Lide (Editor): Handbook of Chemistry and Physics. CRC Press, Boca Raton, 88th Edition 2007-2008; page 4-3.
[2] Hugh Aldersey-Williams: Periodic Tales: a cultural history of the elements, from arsenic to zinc. Harper-Collins Publisher, New York, NY 10022, 2011; page 260 [ tales].

Sunday, March 9, 2014

The aluminum-ore bauxite, named after the village of Les Baux in Provence, France

Les Baux is a small town near St. Reny in the Bouches-du-Rhône department of the province of Provence in southwest France. Les Baux-de-Provence, as this beautiful and scenic village is often named, is a listed heritage site located in the heart of the Alpilles regional country park [1]. Near Les Baux, the ore bauxite was first discovered in 1821 by the geologist Pierre Berthier [2]. In 1847, Armand Dufrénoy named the ore beauxite. In 1861, Henri Sainte-Claire Deville, who discovered a method to separate kilogram amounts of aluminum from the ore's Al-containing constituents böhmite (γ-AlO(OH)), diaspore (α-AlO(OH)) and gibbsite (Al(OH)3), renamed the ore to bauxite [3].

Hugh Aldersey-Williams summarizes the isolation of aluminum (moniker: silver from clay) from bauxite and the metal's usefulness in his Periodic Tales as follows [4]:

This now ubiquitous material—as vital to us as steel and more visible than any of the metals known in antiquity—was only isolated as recently as the 1820s, and it was not until the 1850s that an even remotely commercial way was found to separate it from its ore, bauxite, named after Les Baux in Provence, where it is still possible to see the bleached quarry works on the hill above the town. The process developed by Henri Sainte-Claire Deville in Paris involved heating compounds of aluminium with sodium metal, which was itself exceptionally hard to obtain, and this made his aluminium hugely expensive. Though it scarcely seems credible now, aluminium was hailed as a new precious metal to be placed along with gold and silver—its sheer cost and exoticism compensating for its low density and diffuse shine—and it was worked and flaunted in ways that reflected this status.

Today, the sound of the ore name bauxite can be recognized in many languages—with language-specific variations mostly limited to spelling:
  • Danish: bauxit
  • Dutch: bauxiet
  • Finnish: bauksiitti
  • German: Bauxit
  • Italian: bauxite
  • Polish: boksyt
  • Portuguese: bauxita (or bauxite)
  • Spanish: bauxita

Keywords: mineral name, renaming, place name, locality, aluminium ore, aluminum ore, quarry works, metallurgy, mining, history.

References and more to explore
[1] Les Beaux-de-Provence: One of the most beautiful villages in France [].
[2] Fact Index: Bauxite [].
[3] alu: Bauxite & alumina history [].
[4] Hugh Aldersey-Williams: Periodic Tales: a cultural history of the elements, from arsenic to zinc. Harper-Collins Publisher, New York, NY 10022, 2011; page 255 [ tales].

Thursday, January 30, 2014

An anagram for LOVE: the word VOLE

Voles are small, mouse-size mammals closely related to other rodents such as lemmings. Voles are famously monogamous [1]. The prairie vole, for example, is an animal model for studying monogamous behavior and pair bonding. However, love-making and romance do not always translate simply into a granted male-female relation—at least not from a scientific viewpoint. Abigail Tucker, in a recent Smithsonian article, disclosed a dirty little secret [2]: “Prairie voles are socially, but not sexually, monogamous.

Voles—like other mammals, including humans—exhibit the phenomenon of opportunistic infidelity. Some call it side-stepping, others cheating. And anthropologists have always known that monogamy is not the default condition in human cultures and civilization. The behavior of rejecting a recent and yearning for a new sex partner is dubbed the Coolidge Effect, based on an anecdotal story about John Calvin Coolidge, the 30th President of the United States, visiting a rooster & hen farm [3].

Interestingly, a lot of chemistry is behind how our (and the voles) bonding impulses are switched and wired: it has been found that natural variations in the DNA sequence of the vasopressin receptor gene determine the occurrence of neurochemical receptors in certain brain areas and thus the quality of monogamous or polygynous interaction [2,4]. Non-coding DNA, once misnamed “junk DNA,” plays a significant role in sexual programming.

Prairie vole studies demonstrate that brain chemicals are critical and effective communicators in regulating love, bonding and child care. The chemical messenger compound oxytocin—known as a hormone regulating social-cue perception, childbirth and maternal bonding—and the hormone vasopressin are such chemical candidates that trigger partner bonding [2]:
When a female prairie vole received an oxytocin injection in her brain, she huddled with her partner more and formed stronger bonds. Another hormone, vasopressin, related to territoriality, has been found to promote pair-bonding in males. [...] If the hormones responsible for maternal behavior in females and territoriality in males were released during sex, they could foster this novel male-female bond. Prairie vole sex, for instance, involves an unusual amount of vaginal-cervical stimulation—probably an adapted behavior that triggers the oxytocin release normally associated with childbirth. Instead of bonding with a baby, the female bonds with her partner.
Beyond love: oxytocin—the lack of it—has also been linked with autism-spectrum disorder (ASD) [5].

Keywords: molecular biology, neuroscience, neurochemistry, monogamy, partnership, wanderers, anthropology.

References and more to explore
[1] Bob Yirka: Researchers find epigenetic factor in monogamy for voles. June 3, 2013 [].
[2] Abigail Tucker: Love. What can rodents tell us about why humans love? Smithsonian February 2014, 44 (10), pp. 42-49 [].
[3] Marnia: The Coolidge Effect. June 23, 2005 [].
[4] JUNKDNA [].
[5] Christopher Bergland: The Neurobiology of the “Love Hormone” Revealed. Psychology Today August 5, 2013 [].