History and nomenclature of the Conocardioidea (Mollusca: Rostroconchia)

In this nomenclatural-historical account of the genera of the Conocardioidea (Mollusca: Rostroconchia) several inconsistencies and errors in the taxonomy and nomenclature of the Conocardioidea are clarified.Cardium aliforme J. de C.Sowerby, 1827, is recognised as type species of the genusConocardium Bronn, 1835, according to the ICZN 4^th edition. Based on subsequent incorrect spelling which is in prevailing use, the spellingC. aliforme takes precedence overC. alaeforme andC. aliformis. Further nomenclatural difficulties concerning the generaHippocardia Brown,Pleurorhynchus Phillips,Lichas Steininger andRhipidocardium Fischer are settled. All genus group names and all higher taxa of the Conocardioidea until 2003 are checked from a nomenclatural point of view. The order name Conocardioida is emended herein into Conocardiida as originally used byNeumayr and because it does not conform with Latin grammar.      

History and nomenclature of the theropod dinosaur tracks Bueckeburgichnus and Megalosauripus

The most recent account of Bueckeburgichnus maximus Kuhn 1958, a distinctive theropod dinosaur track from the Lower Cretaceous of Germany, is shown to be based on a referred specimen mistakenly identified as the holotype and the correct name of this taxon is deemed to be Megalosauripus maximus (Kuhn 1958). This minor revision has important consequences for nomenclature of the many European, Asian, North American and Australian dinosaur tracks attributed to megalosaurian theropods. Many of those tracks were named Megalosauripus, but that name has a confusing multiplicity of meanings and it should be restricted to the highly characteristic dinosaur track formerly identified as Bueckeburgichnus. Other tracks named "Megalosauripus”; (in its several other senses) will require new nomenclature, despite their extensive and repeated revision since 1996. It is recommended that future revision should adopt conventions of the International Code of Zoological Nomenclature. Although previous revisions expressed an intention to adhere to those conventions, these were not put into practice, with the unfortunate result of multiplying the problems that surround the nomenclature of megalosaur tracks. Introduction of the name Megalosauripus maximus (Kuhn 1958) eliminates those burgeoning problems and permits the introduction of new and objective nomenclature for presumed megalosaur tracks.     

A nomenclature system for isofurans

Recently, the isolation of a new class of human arachidonic acid oxidation products, the isofurans, was reported. These are produced in vivo by a free radical mechanism independent of the cyclooxygenase enzymes. Because these compounds are tetrahydrofuran derivatives that are related biosynthetically to the isoprostanes, they were termed isofurans. There are eight different isofuran regioisomers, each of which can exist as 16 racemic diastereomers. Thus, 256 enantiomerically-pure isofurans can be formed. These molecules are of interest as measurement of isofurans provides a sensitive index of free-radical induced lipid peroxidation in vivo under conditions of elevated oxygen tension. They also, in analogy to isoprostanes, may have potent biological activity. To explore this, the chemical synthesis of the IsoFs has been initiated. As a result, there is a need for a systematic nomenclature for this class of natural products. A facile system that will allow the ready differentiation of each of the isomeric structures comprising the family of isofurans is presented.     

The grapevine gene nomenclature system

Background

Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, data on structural and functional characterization of grape genes accumulated exponentially. To better exploit the results obtained by the international community, we think that a coordinated nomenclature for gene naming in species with sequenced genomes is essential. It will pave the way for the accumulation of functional data that will enable effective scientific discussion and discovery. The exploitation of data that were generated independently of the genome release is hampered by their heterogeneous nature and by often incompatible and decentralized storage. Classically, large amounts of data describing gene functions are only available in printed articles and therefore remain hardly accessible for automatic text mining. On the other hand, high throughput “Omics” data are typically stored in public repositories, but should be arranged in compendia to better contribute to the annotation and functional characterization of the genes.

Results

With the objective of providing a high quality and highly accessible annotation of grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Super-Nomenclature Committee for Grape Gene Annotation (sNCGGa) to coordinate the effort of experts to annotate the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define conventions for a gene naming system in this paper.

Conclusions

Learning from similar initiatives in other plant species such as Arabidopsis, rice and tomato, a versatile nomenclature system has been developed in anticipation of future genomic developments and annotation issues. The sNCGGa’s first outreach to the grape community has been focused on implementing recommended guidelines for the expert annotators by: (i) providing a common annotation platform that enables community-based gene curation, (ii) developing a gene nomenclature scheme reflecting the biological features of gene products that is consistent with that used in other organisms in order to facilitate comparative analyses.     

Toward a phylogenetic system of biological nomenclature

Despite the widely held belief that modem biological taxonomy is evolutionary, some of the most fundamental concepts and principles in the current system of biological nomenclature are based on a nonevolutionary convention that pre-dates widespread acceptance of an evolutionary world view by more than a century. The development of a phylogenetic system of nomenclature requires reformulating these concepts and principles so that they are no longer based on the Linnean categories but on the tenet of common descent.     

Purine cytokinin nomenclature: a working system of abbreviations

Many synonyms for the cytokinin 6-(benzylamino)purine and its metabolites have arisen in the literature despite a 1970 IUPAC-IUB directive delimiting such nomenclature. Examples of symbols and abbreviations for some classes of this cytokinin are given. The reasons for this continued synonomy are attributed to difficulties associated with the IUPAC-IUB recommendations. A modified system of abbreviations is presented in tabular form and the utility of the scheme discussed.     

Uniform nomenclature for the mitochondrial contact site and cristae organizing system

The mitochondrial inner membrane contains a large protein complex that functions in inner membrane organization and formation of membrane contact sites. The complex was variably named the mitochondrial contact site complex, mitochondrial inner membrane organizing system, mitochondrial organizing structure, or Mitofilin/Fcj1 complex. To facilitate future studies, we propose to unify the nomenclature and term the complex “mitochondrial contact site and cristae organizing system” and its subunits Mic10 to Mic60.Mitochondria possess two membranes of different architecture and function (Palade, 1952; Hackenbrock, 1968). Both membranes work together for essential shared functions, such as protein import (Schatz, 1996; Neupert and Herrmann, 2007; Chacinska et al., 2009). The outer membrane harbors machinery that controls the shape of the organelle and is crucial for the communication of mitochondria with the rest of the cell. The inner membrane harbors the complexes of the respiratory chain, the F₁F_o-ATP synthase, numerous metabolite carriers, and enzymes of mitochondrial metabolism. It consists of two domains: the inner boundary membrane, which is adjacent to the outer membrane, and invaginations of different shape, termed cristae (Werner and Neupert, 1972; Frey and Mannella, 2000; Hoppins et al., 2007; Pellegrini and Scorrano, 2007; Zick et al., 2009; Davies et al., 2011). Tubular openings, termed crista junctions (Perkins et al., 1997), connect inner boundary membrane and cristae membranes (Fig. 1, A and B). Respiratory chain complexes and the F₁F_o-ATP synthase are preferentially located in the cristae membranes, whereas preprotein translocases are enriched in the inner boundary membrane (Vogel et al., 2006; Wurm and Jakobs, 2006; Davies et al., 2011). Contact sites between outer membrane and inner boundary membrane promote import of preproteins, metabolite channeling, lipid transport, and membrane dynamics (Frey and Mannella, 2000; Sesaki and Jensen, 2004; Hoppins et al., 2007, 2011; Neupert and Herrmann, 2007; Chacinska et al., 2009; Connerth et al., 2012; van der Laan et al., 2012).Open in a separate windowFigure 1.MICOS complex. (A) The MICOS complex (hypothetical model), previously also termed MINOS, MitOS, or Mitofilin/Fcj1 complex, is required for maintenance of the characteristic architecture of the mitochondrial inner membrane (IM) and forms contact sites with the outer membrane (OM). In budding yeast, six subunits of MICOS have been identified. All subunits are exposed to the intermembrane space (IMS), five are integral inner membrane proteins (Mic10, Mic12, Mic26, Mic27, and Mic60), and one is a peripheral inner membrane protein (Mic19). Mic26 is related to Mic27; however, mic26Δ yeast cells show considerably less severe defects of mitochondrial inner membrane architecture than mic27Δ cells (Harner et al., 2011; Hoppins et al., 2011; von der Malsburg et al., 2011). The MICOS complex of metazoa additionally contains Mic25, which is related to Mic19, yet subunits corresponding to Mic12 and Mic26 have not been identified so far. MICOS subunits that have been conserved in most organisms analyzed are indicated by bold boundary lines. (B, top) Wild-type architecture of the mitochondrial inner membrane with crista junctions and cristae. (bottom) This architecture is considerably altered in micos mutant mitochondria: most cristae membranes are detached from the inner boundary membrane and form internal membrane stacks. In some micos mutants (deficiency of mammalian Mic19 or Mic25), a loss of cristae membranes was observed (Darshi et al., 2011; An et al., 2012). Figure by M. Bohnert (Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany).To understand the complex architecture of mitochondria, it will be crucial to identify the molecular machineries that control the interaction between mitochondrial outer and inner membranes and the characteristic organization of the inner membrane. A convergence of independent studies led to the identification of a large heterooligomeric protein complex of the mitochondrial inner membrane conserved from yeast to humans that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane (Fig. 1 A). Several names were used by different research groups to describe the complex, including mitochondrial contact site (MICOS) complex, mitochondrial inner membrane organizing system (MINOS), mitochondrial organizing structure (MitOS), Mitofilin complex, or Fcj1 (formation of crista junction protein 1) complex (Harner et al., 2011; Hoppins et al., 2011; von der Malsburg et al., 2011; Alkhaja et al., 2012). Mitofilin, also termed Fcj1, was the first component identified (Icho et al., 1994; Odgren et al., 1996; Gieffers et al., 1997; John et al., 2005) and was observed enriched at crista junctions (Rabl et al., 2009). Mutants of Mitofilin/Fcj1 as well as of other MICOS/MINOS/MitOS subunits show a strikingly altered inner membrane architecture. They lose crista junctions and contain large internal membrane stacks, the respiratory activity is reduced, and mitochondrial DNA nucleoids are altered (Fig. 1 B; John et al., 2005; Hess et al., 2009; Rabl et al., 2009; Mun et al., 2010; Harner et al., 2011; Head et al., 2011; Hoppins et al., 2011; von der Malsburg et al., 2011; Alkhaja et al., 2012; Itoh et al., 2013). It has been reported that the complex interacts with a variety of outer membrane proteins, such as channel proteins and components of the protein translocases and mitochondrial fusion machines, and defects impair the biogenesis of mitochondrial proteins (Xie et al., 2007; Darshi et al., 2011; Harner et al., 2011; Hoppins et al., 2011; von der Malsburg et al., 2011; Alkhaja et al., 2012; An et al., 2012; Bohnert et al., 2012; Körner et al., 2012; Ott et al., 2012; Zerbes et al., 2012; Jans et al., 2013; Weber et al., 2013). The MICOS/MINOS/MitOS/Mitofilin/Fcj1 complex thus plays crucial roles in mitochondrial architecture, dynamics, and biogenesis. However, communication of results in this rapidly developing field has been complicated by several different nomenclatures used for the complex as well as for its subunits (