Monday, May 13, 2013

Synonyms for sand corn, the common name of a flowering plant native to the western United States and parts of New Mexico

Sand-corn (Zigadenus paniculatus), also named foothill or panicled deathcamas
Sand corn is a flowering plant found in dry habitats of the western United States; for example in northwest Nevada. It has two accepted scientific names: Zigadenus paniculatus (Nutt.) S. Watson and  Toxicoscordion paniculatum (Nutt.) Rydb. [1-5].  Its scientific classification: order Liliales. In the literature, sand corn is taxonomically grouped either into Lilliaceae (lily family) or Melanthiaceae, the latter not unanimously recognized as a family and sometimes considered as part of the lily family.

Sand corn, also written sand-corn, is often referred to by its other common name: foothill deathcamas (also written: foothill death camas). This name indicates the poisonous character of the plant, which becomes relevant, when sand corns are growing on rangeland: intoxication of livestock may result from their alkaloid components such as zygacine [3].

Another synonym, panicled death camas [4], makes a reference to the often bending or nodding panicle with sometimes over fifty flowers (see Thomas Creek plant)—each having six small tepals with yellow-green splotch at base and showy, yellow anthers [5].

Keywords: botany, taxonomy, nomenclature, scientific name.

References and more to explore
[1] USDA Plants Profile: Zigadenus paniculatus (Nutt.) S. Watson [].
[2] Kew Royal Botanic Garden: Toxicoscordion paniculatum (Nutt.) Rydb., Bull. Torrey Bot. Club 30: 272 (1903) [].
[3] K. D. Welch et al.: The acute toxocity of the death camas (Zigadenus species) alkaloid zygacine in mice, including the effect of methyllycaconitine coadministration on zygacine toxity. J. Anim. Sci. 2011, 89 (5), pp. 1650-1657.  
doi: 10.2527/jas.2010-3444.
[4] Calflora Taxon Report 8367:  Zigadenus paniculatus [].
[5] Laird R. Blackwell: Tahoe Wildflowers. Morris Book Publishing, LLC, Guilford, Connecticut, 2007; page 37.

Tuesday, May 7, 2013

A term in microbial ecology: disappearing microbiota hypothesis

Occurrences of certain medical conditions and diseases such as asthma, food allergies, hay fever, eczema, diabetes, obesity and celiac disease are dramatically going up. The physician and director of the Human Microbiome Program, Martin Blaser at New York University's School of Medicine is hypothesizing that the disappearance of microbiota from the human body is to blame. This loss of  microbiome species is largely caused by our obsessive use of antibacterial soaps and lotions as well as frequent treatments with antibiotics [1,2]:
Though they have always known that antibiotics kill “good” bacteria as well as “bad,” doctors generally assumed the body's microbial community was resilient enough to bounce back. But new studies show that the microbiome struggles to recover from repeated assaults, and may lose species permanently. Blaser suspects that diversity loss is cumulative, worsening from one generation to the next. He calls it “the disappearing microbiota hypothesis.” [boldface by author]
How clean should we be, without cleaning out the good microbes—or disturbing the balance between good, bad and neutral ones—that live behind our ears, in our armpits and in our gut and mouth?

Keywords: microbial diversity, microbiome, microbiology, medicine, hygiene, human health.

References and more to explore
[1] Martin J. Blaser, M. D. [].
[2] Richard Conniff: The Body Eclectic. Smithsonian May 30, 2013, 44 (2), pp. 40-47 [].

Friday, May 3, 2013

Trendy and inspirational: the suffixes -ome and -omics

In the beginning there was the word genome for the complete set of genetic material present in a cell or organism. The German botanist Hans Winkler came up with this term in 1920 [1]. It is a portmanteau blending the words gene and chromosome. An Oxford Dictionary of 2002 further tells us that [2]:

a  couple of terms have been formed on its model [the portmanteau genome]: proteome, the complete set of proteins produced from the instructions coded in a cell's genetic material, and metabolome (from metabolism), the complete set of metabolic processes within a cell. These seem to have been created partly by blending and partly by analogy with the older sense of the ending.

The older sense of -ome is the meaning of having a specified nature; for example, rhizome for the subterranean roots and shoots of a plant [2].

Now, ten years later, there are hundreds or even thousands of words derived by following the nomenclatural model creating the established terms genome, proteome and metabolome. The word transcriptome refers to the set of RNA molecules expressed from the genome. Emerging terms include variome for the set of genetic variation across a population of a species, epigenome for the set of chemical compounds involved in not-DNA-encoded gene expression, interactome for the set of molecular interactions in a biological system such as a cell, and fluxome for the set of small molecules changing along metabolic pathways in a dynamic system (due to flux responses resulting from both genetic and metabolic regulation). Terms you certainly will find more often in future publications include phenome for the set of physical descriptions that can ideally be related to genotype, regulome for the set of regulatory compounds in a cell, integrome for unions of 'omics data sets, omnisciome for the entirety of knowledge about a cell, organism or system, toxome for the set of cellular processes responsive to small molecules and involved in their toxicological activities, and lipidome for the set of all fatty molecules in an organism [3].

The name of a scientific field associated with an ome-ending word is typically built by replacing the suffix -ome with -omics. Genomics, proteomics, and metabolomics are well known examples. Transcriptomics, variomics, epigenomics, interactomics, fluxomics, phenomics, regulomics, integromics and lipidomics are emerging names and disciplines of scientific study. Omnisciomics and toxomics may follow. Data and knowledge within these fields have not all been derived from recent studies, some insight has been accumulated over decades. But recent advances, driven by modern analytical devices and high-throughput technology, are accelerating application and impact of these fields. Dedicated to the integration of  'omics domains is a peer-reviewed journal with the name OMICS [4].

And then there is the ending -etics, as in genetics. The distinction between 'omics and 'etics may seem confusing for outsiders. Let's conclude this with the description of the fine line between epigenomics and epigenitcs [5]: “Epigenetics focuses on processes that regulate how and when certain genes are turned on and turned off, while epigenomics pertains to analysis of epigenetic changes across many genes in a cell or entire organism.”

Keywords: biochemistry, linguistics, nomenclature, terminology, meta-data, integrative research.

References and more to explore
[1] Where the Word 'Genome' Came From [].
[2] Michael Quinion: Ologies and Ismas. A Dictionary of Word Beginnings and Endings. Oxford University Press, Oxford and New York, 2002..
[3] Monya Baker: The 'omes puzzle. Nature February 28, 2013, 494, pp.416-419. doi: 10.1038/494416a
[4] OMICS: A Journal of Integrative Biology [].
[5] National Cancer Institute: Epigenomics and Epigenetics Research [].