A New Nomenclature

In 1787, the Academie Royale des Sciences in Paris published a book entitled Meth-ode de nomenclature chimique The front page names four authors Louis-Bemard Guyton de Morveau, Antoine-Laurent Lavoisier, Claude Louis Berthollet, and Antoine Francois Fourcroy. In this book, one encounters the first comprehensive classification of chemical substances according to composition in the history of chemistry. Taking into account the stature of its authors, its proximity in time to Lavoisier s Trade elementaire de chimie from 1789, and the fact that it first appeared in a book on chemical nomenclature, this classification immediately raises a variety of questions and issues. 

To answer these questions, a thorough and detailed investigation of the chemical classification from 1787 is required. Before beginning our scrutiny of the table, it may be fitting to first inform ourselves more about the nomenclatural enterprise in the framework of which this classification came about. 

For bibliogra Mc infonnadon on Fiencfa editions as well as contemporary translations of this book, see Abbri and Beretta [1995] for assessments and discussions of the Methode see Anderson [1984] chapter 7 BensaQde- cent [1983], [1994], and [1995] Beretta [1993] chapter 4, and [2000] Crosland [1962] part IB Dagognet [1969] part I Go[inski [1992] Risldn [1998] Roberts [1992] Siegfried [2002] chapter 11 and Smeaton [1954], 

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The discovery of this evolutionary activity has reeked havoc with the accepted PTS protein nomenclature. Instead of the time-honored E-I, E-II, E-III and HPr, we must resort to cumbersome phrases such as the E-III-like domain of E-IT etc. To alleviate the problem, Saier Jr and Reizer [3] have proposed a new nomenclature (Fig. 2) based on the original IIA/IIB nomenclature of Kundig and Roseman [4]. The old nomenclature is given above the bars representing the permeases in Fig. 2 and the new nomenclature below the bars. H and I still represent HPr and E-I, respectively, but IIA replaces E-IIl. IIC represents the hydrophobic domain of E-... 

Keratins are alpha-type fibrous polypeptides with a diameter of 7 11 nm. They are important components of the cytoskeleton in almost all epithelial cells as well as in some nonepithelial cell types. Keratins are generally held to be the most ubiquitous markers of epithelial differentiation. So far, 20 distinct types numbered by Moll et al. (1982a, 1990, 1992) have been revealed. Keratins were earlier thought to be separable into hard and soft, or cytokeratins and other keratins, but these designations are now understood to be incorrect. In 2006, a new nomenclature (Schweizer et al. 2006) was adopted for describing keratins which takes this into account (Table 13.1). 

It is generally accepted that three major classes of opioid receptors exist. The most commonly used terminology discriminates between p-, K-, and 8-opioid receptors. However, after cloning of the three genes encoding opioid receptors, a new nomenclature was agreed upon OPl (corresponding to the 8 receptor), OP2 (k receptor) and OP3 (p receptor) (Dhawan et ah. 

A new nomenclature was therefore designed to describe the subtypes of IFN rather than naming them for the source from which they were originally isolated. The designation of huIFN-a was suggested for the major class of IFNs present in leukocyte or lymphoblastoid preparations. huIFN-P was used to denote IFN produced by fibroblasts, and huIFN-y was assigned to human immune IFN produced by activatedT-lymphocytes [25] (Table 7.2). 

During the course of developing several theories concerning the nature of quarks, physicists required a new nomenclature, To persons outside the... 

JM Jez, TG Flynn, TM Penning. A new nomenclature for the aldo-keto reductase superfamily. Biochem Pharmacol 54 639-647, 1997. 

He contributed to the formulation of a new nomenclature in chemistry, based on his understanding of simple substances and on a clear recognition that certain combinations of simple substances were stable, persevering through a series of reactions. 

More recently, a third omics field, lipidomics, was developed. Lipidomics was developed to attempt to provide a system in which to quantitatively profile all of the lipid molecules in a given species or in a tissue within that species (Han, 2011 Welti, 2011). Not surprisingly, a new nomenclature system has been developed to help to define and catalog the various lipids in the lipidome of each species. In this system, tocopherols and tocotrienols are part of the category called prenols (Table 11.1). Currently, the main database for lipidomics information in the USA is the LIPID-MAPS (2011) and its Prenol category contains the four known tocopherols (oc, (3, y, 5), four known tocotrienols (a, [3, y, 5), and a total of 1177 Prenols. Each of the eight individual tocopherols and tocotrienols are sometimes referred to as vitamers. 

A scientific theory, like a mathematical system, never yields more than is built into it in the way of assumptions or postulates. The phenomenological approach presented in the preceding chapters could no more than characterize the kinetic behavior of systems in terms of the macroscopic variables used to describe them. We have obtained from this approach the kinetic quantities and rate constants or, in terms of the Arrhenius formulation, the frequency factors and the energies of activation. These quantities constitute our phenomenological category of kinetic language. If we are to relate them to the molecular properties of the reacting species, we must construct a new theory and a new nomenclature which starts with the molecule as the unit under consideration. 

A new nomenclature of HE existing since 2002 distinguishes three forms (7.) type A (= HE associated with acute liver failure), (2.) type B (= HE associated with portosystemic bypass without liver disease), and (2.) type C (= HE associated with liver cirrhosis). 

Figure 1. Condensed phylogenetic tree of the coronin protein family. The tree constitutes the basis of a new nomenclature and shows the evolutionary relationship of the twelve coronin subfamilies (CRN1-CRN12). See also chapter 11-2 by Reginald O. Morgan and M. Pilar Fernandez.

When Arrhenius focused attention on ions as well as molecules, it became necessary to name charged particles in addition to neutral species. It was not deemed necessary to develop a new nomenclature for salts cations were designated by the names of the appropriate metal and anions by a modified name of the non-metal portion. 

Berthollet, Morveau, and Fourcroy, decided to formulate a new nomenclature for chemistry based on Lavoisier s work. They believed that to reform chemistry, it had to be reformed completely, with a new language of chemistry for a new system of chemistry. Their work was published in 1787 as Methode de nomenclature chimique. It is from this work that the modern system of naming chemicals developed. It introduced word endings like -ic to represent acids and -ide to indicate oxides. 

Recently, the HUGO Gene Nomenclature Committee adopted a new nomenclature, the SLCO (character O is from the head letter of OATP). It is subdivided into families (>40% amino acid sequence identity), subfamilies (>60% amino acid sequence identity), and individual genes and gene products according to their phylogenetic relationships and chronology of identification [2]. 

We can define a new quantity, the kinetic heat capacity CpK = C/AMHR. The complete deconvolution then gives rise to a new nomenclature ... 

While genotyping may seem useful, the models that are developed may only be applicable until a new nomenclature is used or another defective allele is identified. For example, in 2001, when Kirchheiner et al. 

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