A botanic garden acronym: CUBG for Cambridge University Botanic Garden

CUBG stands for Cambridge University Botanic Garden. Botanic gardens and arboreta always are great places to study plants, to follow their changes over the cycle of seasons and to get excited about biodiversity—or phytodiversity in this case.

What is so special about the CUBG is that it is backed up by a chemical trail: a virtual trail that provides quick access to a detailed, web-based description of selected flowers and trees and further identifies some plant ingredients,  chemical compounds, that play a role in and have been extracted for human uses. Drugs, dyes, and natural food additives are just a few examples. To explore the featured plants and substances, I recently published a post and some visual navigation tools:

• List of chemical plant ingredients in my post A walk through plant chemistry,
• Plant Life board with pictures and links for the chemical trail plants: pinterest.com/axeleratio/plant-life/, 
• Learn chemistry while traveling board with the molecular structure of phytochemicals:  pinterest.com/axeleratio/learn-chemistry-while-traveling/.

Keywords: botany, plant chemistry, plant ingredients, phytochemistry, biochemistry, garden tour.

Question: Are there other gardens of this kind? See ResearchGate Question.

A term in chemistry: elementary substance

An elementary substance is a pure chemical substance that consists of atoms belonging to a single chemical element. Otherwise, if atomic species from different chemical elements are involved in composing a substance, chemists speak of a compound.

The term “elementary substance” is further used to distinguish a chemical substance that is composed of same-element atoms (atoms with the same number of protons in the atomic nucleus) from the chemical element itself. The latter includes all species of atoms (atoms, ions, radicals) that have the same number of protons in the atomic nucleus [1].  It has been suggested that only this latter concept should be employed when referring to a chemical element: the term “element” should be reserved to collectively designate all atomic forms of an element [2]. Then, any molecule-building or other combination of atomic forms of an element constitutes an elementary substance.

Example: The allotropes dioxygen (O₂) and ozone (O₃) are elemenary substances of the chemical element oxygen. Isotopically labelled dioxygen species such as [¹⁶O][¹⁷O] and other polyatomic species based merely on oxygen isotopes also are elementary substances. On the other hand, water (H₂O) is a chemical compound, since it consists of atoms belonging to two different elements—oxygen and hydrogen.

Keywords: chemistry, chemical education, terminology, IUPAC definition, chemical element, chemical compound, homonuclear molecule.

References
[1] Gold Book: chemical element [goldbook.iupac.org/C01022.html].
[2] Rollie J. Myers: What Are Elements and Compounds? J. Chem. Educ. 2012, 89, pp. 832-833. DOI: 10.1021/ed200269e.

German for casual travelers: Schon 'was zum Pennen?

“Schon 'was zum Pennen?” is short for “Schon etwas zum Pennen?”
The vocabulary:

• schon: already
• etwas: something
• zum: to 
• pennen: to nap or to sleep

The question “...schon 'was zum Pennen?” is asking you, if you have found a place to stay overnight.  Painting and question are found at the south-facing wall of the Zollhaus Bremen, Am Kaffee-Quartier 1, Walle, 28217 Bremen.

This former custom-house (Zollhaus) in Bremen's  harbor district has been turned into a hostel (www.zollhaus-bremen.de). With the slogan “Meet and sleep in Bremen,” the Zollhaus invites easy-going travelers to stay at this affordable hotel. Bremen's city center, the Weser river walk and biking promenade, the still developing harbor city (Überseestadt) as well as coffee shops, bistros, restaurants, pubs and other hang-outs are nearby—a short walk or bike ride away. Lots to do and not much time “zum Pennen.”

Keywords: German slang, tourism, city of Bremen, harbor district.

English-German word play: “umfairteilen” sounds like “umverteilen”

The adjective fair can take on various meanings in English, including the meaning of being honest, impartial and just—as in the phrase fair play. When used in German, fair has that meaning. The word fair sounds like the German prefix ver, giving rise to the word play of the trade-union banner above, where the verb umfairteilen is used instead of umverteilen. The meaning of the latter should become clear by comparing the meaning of the simple verb teilen with those of the composita that are derived by employing the prefixes ver and um:

• teilen: divide
• verteilen: distribute or share
• umverteilen: redistribute

The verb umfairteilen has cleverly been constructed to ask for a fair redistribution of wealth. The text umfairteilen - Reichtum besteuern, displayed over the entrance of the Gewerkschaftshaus Bremen (trade union building in Bremen in northern Germany), calls for the redistribution of wealth via adjusted tax regulations. The noun Reichtum means riches or wealth and the verb besteuern means to tax.

Keywords: Wortspiel, word play;  Steuern, taxes; Politik, politics;  soziale Gerechtigkeit, social justice.

Detailed information on Germany's Umfairteilen activities and demands is given at de.wikipedia.org/wiki/Umfairteilen.

Mastigostyla woodii in the iris family named in honor of British botanist John Wood

 Mastigostyla woodii, a Bolivian plant in the iris family (Iridaceae) with blue-purple flowers, was named in honor of the British botanist John R. I. Wood [1-3]. The genus name is based on the greek words mastigos and stylos, meaning “whip” and “style,” respectively. The conservation status and distribution of M. woodii and the three related species M. cardenasii, M. chuquisacensis and M. torotoroensis in the arid mountains and valleys of the eastern Andes in Boliva has recently been described [4].

John Wood, an Honorary Research Associate at Kew, collected plant specimens from around the world, including habitats in Yemen, Bhutan, Columbia and Bolivia. Wood collected more than 30,000 plant specimens over 40 years and encountered various inconveniences during his search for remote places and rare species. He had malaria twice, Dengue fever once, and is today celebrated as an elite field botanists—a discoverer and science-driven gatherer from an era that is drawing to a close [3].

Taxonomy of Mastigostyla woodii Huayalla & Wilkin [1]
Class: Equisetopsida
Subclass: Magnoliidae
Superorder: Lilianae
Order: Asparagales
Family: Iridaceae
Note that the above organization is based on the Angiosperm Phylogeny Group (APG) system, while the Cronquist, Takhtajan or Thorne system treat Iridaceae as part of the order Liliales, Iridales or Orchidales, respectively.

Keywords: botany, systematics, nomenclature, plant collecting.

References and more to explore
[1] Kew Royal Botanical Gardens: Mastigostyla woodii [www.kew.org/plants-fungi/Mastigostyla-woodii.htm].
[2] Encyclopedia of Life: Mastigostyla woodii [eol.org/pages/31921821/details].
[3] John Whitfield: Rare Specimens. Nature April 25,  2012, 484, pp. 436-438 [www.nature.com/news/superstars-of-botany-rare-specimens-1.10498].
[4] Hibert Huaylla, Paul Wilkin and Odile Weber: Mastigostyla I. M. Johnst. in Bolivia: three new species and new data on M. cardenasii R. C. Foster. Kew Bulletin June 2010, 65 (2), pp. 241-254. doi: 10.1007/s12225-010-9199-y.

Molecular-modeling terms in pharmacology: ADMET, ADME and ADME-Tox

The acronym ADMET stands for absorption, distribution, metabolism, elimination, and toxicity. The word elimination may be swapped for excretion. This acronym is typically used in the context of drug design, where the relationship between the molecular structure and properties of chemical substances with pharmacokinetic, metabolic and toxicological endpoints is key in finding promising candidates to be further explored and tested as drugs. Toxicity—seen as a result of the other for processes or phenomena—is sometimes considered separatedly and the acronym ADME without a final T for toxicity is then used. Or, the notation ADME-Tox (also: ADME/Tox) is employed, visually separating the role of toxicity from the four physiological functions.

A short introduction and important links to ADMET-integrated research and associated software tools have recently been posted online. 

An acronym in genetics: SNP for single nucleotide polymorphism

In genetics, the acronym SNP stands for single nucleotide polymorphism. SNP is pronounced “snip” [1-4] .

SNPs are recognized by comparing aligned sequences of DNA. A single location along a pair of “matching” sequences, at which two nucleotides differ, constitute a SNP. In the above example, the swap of thymine (T) for adenine (A) is such a SNP.

SNPs are biological markers in the genome of humans and other life forms. SNP comparison—by using human genomes from distinct populations around the world—helps to understand genetic diversity of humans and, for example, regiospecific disease patterns and human adaption to different environments.

A recent article by Gary Styx illustrates the role of SNP in studying the historical path of human migration around the globe all the way to contemporary human diversity [5].

Keywords: bioinformatics, evolutionary anthropology, ancestry, DNA building blocks, diversity of DNA

References and more to explore
[1] An earlier SNP post on Latintos: http://golatintos.blogspot.com/2010/10/acronym-in-genomics-snp-for-single.html.
[2] Genetics Home Reference: What are single single nucleotide polymorphisms (SNPs)? [ghr.nlm.nih.gov/handbook/genomicresearch/snp].
[3] SNPedia: Single Nucleotide Polymorphism [snpedia.com/index.php/Single_Nucleotide_Polymorphism].
[4] National Human Genome Research Institute/Francis S. Collins: Single Nucleotide Polymorphisms (SNPs) [www.genome.gov/Glossary/index.cfm?id=185].
[5] Gary Styx: Traces of a Distant Past. Scientific American Winter 2013, 22 (1), 60-67.