Problems in nomenclature of craniofacial disorders

The diverse background of clinical geneticists may lead to problems of communication unless attention is paid to nomenclature. In this paper, consensus is sought on terms for normal and abnormal development, a system for labeling developmental defects of dentin is proposed, and terms for patterns of coexistent variations are defined. The major methods for naming coexistent variations are reviewed, with attention to the disadvantages of each. An informal study on recognition of patterns of variation based on the naming system used is also presented.     

Species names in phylogenetic nomenclature

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.     

Isoprostane nomenclature: Inherent problems may cause setbacks for the development of the isoprostanoid field

Do we have to bother about the isoprostane nomenclature? The widely accepted IUPAC isoprostane nomenclature provides an unambiguous and systematic terminology to name all theoretical possible isoprostanes. However, the currently accepted nomenclature system provides an unnatural framework which is not well suited to address certain biologically relevant questions. Artificial categorization of isoprostanoids into prostanoid families disrupts prostaglandin-ring core structures needed to describe biogenetic precursor–product relationships. In addition, the IUPAC system defines isoprostanoid families which comprise chemically heterogeneous isoprostanoids which largely differ in their physicochemical properties from those of the corresponding prostaglandins. As a result of this, alternative nomenclature systems such as the phytoprostane nomenclature system overcoming some inherent problems of the IUPAC nomenclature are still in use. However, different naming of isoprostanoids especially the classification of prostanoid family names has created considerable confusion. Therefore, a cautionary note on the current use of different nomenclature systems is necessary.     

The nomenclature and conformational analysis of lipids and lipid analogues

Lipids form an essential part of the biomembrane and it is of paramount importance to study their conformational aspects. It is found that the present methods of nomenclature for lipids are totally inadequate for describing these diverse amphipathic molecules. Further the existing methods are incompatible in terms of assignment of the absolute configuration. A systematic method for the naming of lipids which is rationally extendible to a wide class of amphipaths is described. The conformational features of the natural glycerolipids as well as a synthetic amphipath containing a glutamic acid moiety known to undergo interesting phase transitions, have been examined in detail using the framework of the current nomenclature system. The implications of the conformational flexibility of these molecules on assemblies of these systems is touched upon.     

SLAⅠ类基因最新命名进展

介绍了国际动物遗传学会（ISAG）SLA命名委员会2004年制定的依据基因测序及进化树分析的SLAⅠ类基因系统命名法,详细叙述了对SLAⅠ类基因座、等位基因组、等位基因及单倍型的命名规则,其中概括介绍了命名新等位基因对基因序列的具体要求。SLAⅠ类基因系统命名法对于人类移植免疫学、猪免疫遗传及抗病育种具有重要意义。     

Uncovering trends in gene naming

We take stock of current genetic nomenclature and attempt to organize strange and notable gene names. We categorize, for instance, those that involve a naming system transferred from another context (for example, Pavlov’s dogs). We hope this analysis provides clues to better steer gene naming in the future.     

A Genetic Nomenclature for Parasitic Nematodes

A uniform system of genetic nomenclature for parasitic nematodes is presented. Conventions for naming strains, genes, alleles, and loci identified as DNA polymorphisms are established, and a standardized system for naming molecular clones is proposed.     

Towards a new classification of Leguminosae: Naming clades using non-Linnaean phylogenetic nomenclature

The past three decades of research have greatly advanced our understanding of phylogenetic relationships in the family Leguminosae. It has become clear in recent years that our classification system is in need of significant updating if it is to reflect our current understanding of the phylogeny of the family and facilitate effective communication of that knowledge. The goal of this paper is to suggest a set of guidelines for formally defining and naming clades, which draws on many of the recommendations embodied in the draft International Code of Phylogenetic Nomenclature or “PhyloCode”. I provide specific examples of phylogenetic nomenclature applied to several well recognized and well-supported, informally named papilionoid clades to serve as a model for standardizing legume clade names by the legume community in the future. For the most part the clades named here are below subfamily and above tribal ranks in the Linnaean system. It is my contention that a new Linnaean classification, designed to reflect phylogeny, and a clade-based system of phylogenetic nomenclature are mutually complementary approaches to achieving a new classification of the legume family.     

国际植硅体命名法规(International Code for Phytolith Nomenclature 1.0)的介绍与讨论

随着植硅体分析的广泛应用,植硅体命名规范化已经成：勾趋势。文章对国际植硅体命名法规中植硅体类型划分、命名和描述的方法与术语进行介绍,提供部分中文对应译名,并对该法规中存在的问题进行探讨,以期引起国内学术界的重视,为我国植硅体命名规范化提供参考。     

"Protistan" nomenclature: analysis and refutation of some potential objections

The nomenclature used for higher taxonomic categories of protista arose under the influence of the two-kingdom system, and is widely recognized as being evolutionarily misleading. The occurrence and promulgation of multiple, contradictory taxonomic systems have added to the confusion. Recently, we proposed a solution to this problem which involves identifying the largest taxa that are widely recognized to be monophyletic, and naming them using a commonly recognizable prefix and the suffix "protista". Thus, nomenclatural prejudice is eliminated, and, by keeping the system informal and thus circumventing the Linnaean system, our system remains flexible in accommodating new data yet should retain a great degree of stability. Here we discuss possible criticisms of our proposal, such as whether the introduction of more terms could lead to further taxonomic and nomenclatural instability, and conclude that our proposal remains a most reasonable solution to the problem of protistan nomenclature.     

A standardized kinesin nomenclature

In recent years the kinesin superfamily has become so large that several different naming schemes have emerged, leading to confusion and miscommunication. Here, we set forth a standardized kinesin nomenclature based on 14 family designations. The scheme unifies all previous phylogenies and nomenclature proposals, while allowing individual sequence names to remain the same, and for expansion to occur as new sequences are discovered.     

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.     

Naming diversity in an evolutionary context: Phylogenetic definitions of the Roucela clade (Campanulaceae/Campanuloideae) and the cryptic taxa within

In recent times, evolution has become a central tenet of taxonomy, but nomenclature has consistently been decoupled from the tree‐thinking process, often leading to significant issues in reconciling traditional (Linnaean) names with clades in the Tree of Life. Recent evolutionary studies on the Roucela clade, a group of endemic plants found in the Mediterranean Basin, motivated the establishment of phylogenetic concepts to formally anchor clade names on the Campanuloideae (Campanulaceae) tree. These concepts facilitate communication of clades that approximate traditionally defined groups, in addition to naming newly discovered cryptic diversity in a phylogenetic framework.     

A proposed unified nomenclature for the enamelled components of the molar teeth of the Cricetidae (Rodentia)

The primitive topography of the enamelled surface of molar teeth of the Cricetidae is described as expressed in the fossil Cricetodontinae. Morphological variations in the molar structure of different subgroups among the Cricetidae are interpreted as derivations from this cricetodontine pattern. Eleven available naming systems for such components are surveyed, and a new unifying nomenclature is proposed, based on the Cope-Osborn cusp homologies for mammals. Names for enamel cusps, cuspules, styles, lophs, folds and islands are given, in an attempt to include in an overall general nomenclature the advantages of the most valuable, already available, nomenclatorial systems. The system purports to apply to all modifications of the cricetid crown molar pattern, and it claims to fulfil the need for a uniform nomenclature.     

浅评当今植物系统学中争论的三个问题——并系类群、谱系法规和系统发育种概念

一般来讲,进化学派承认分支学派对系统学的研究作出了有意义的贡献,如应用分支分析方法重建系统发育,应用共有衍征确定分类群之间的分支关系以及应用外类群方法来判断性状的极性等,都对系统学的方法有所改进。但分支学派的致命缺点是拒绝接受并系类群。我们属于进化学派,认为并系类群是可以接受的。例如,根据分子资料分析,Zabelia属可以包括于Abelia属内。Zabelia属不但在花粉上和Abelia属不同,可能由于它占有了新的生态位,获得了新的特征,如叶柄基部膨大两两联合,并宿存以保护腋芽。有理由认为它们应独立成属,并不由于Zabelia属从Abelia属分出而使后者成为一个并系类群而把它们合并。分支学派的一些学者认为生物名称作为交流的工具和生物信息储存系统应有明晰的、唯一的和稳定的特性。但具等级的林奈命名系统并不具有这些特性来命名分支和种。最后,PhyloCode被提出。PhyloCode对分支的命名方法有3种,即分支结点定义、分支基干定义和衍征定义。我们认为林奈命名系统作为传媒系统在生物学界的应用已近250年,若要废弃它而采用PhyloCode,必然会在命名方面引起一片混乱。但我们并不是说PhyloCode的拥护者所提出的建议一无是处,我们建议他们宜继续进行研究。由于应用生物学种概念于植物界产生了许多问题,因此多为植物系统学家所抛弃。分支学派的兴起,推动了系统发育种概念的提出。该概念基于3个特征,即自征、区别特征和基本排它,因此分别命名为自征种概念、特征种概念和谱系种概念。事实上,目前大多数植物系统学家仍然应用着形态–地理学种概念,但我们在划分种时,必须有尽可能多的资料,特别是要将传粉、繁育系统、分子系统学资料和形态学资料结合起来。     

Paraphyletic group,PhyloCode and phylogenetic species—the current debate and a preliminary commentary

In this essay, three currently hotly debated issues in biological systematics, i.e., the paraphyletic group, the PhyloCode, and the phylogenetic species concept, have been briefly reviewed. (1) It is widely acknowledged that cladistics has made some positive contributions to the study of systematics. In particular, the employment of outgroup analysis for assessing character polarities, the application of synapomorphies to the inference of relationships between taxa, and the use of cladistic methods for reconstructing phylogeny, have all greatly facilitated the improvement of systematic approaches. A fatal flaw in cladistics is its refusal to accept paraphyletic groups. Frankly, we are adherents and practitioners of phyletics, and hence consider paraphyletic groups to be acceptable. For example, an AFLP analysis has shown that Zabelia (Caprifoliaceae) can be included in Abelia, but the members in Zabelia differ from those in Abelia not only in pollen morphology, but also in having persistent petioles dilated and connate at base, thus enclosing axillary buds, characters of adaptive significance obtained possibly when Zabelia members entered a new ecological niche, so we consider that they are better treated as two independent genera, though indeed such a treatment makes Abelia paraphyletic. (2) Some cladists pointed out that as the tool for communication and the system for information storage and retrieval, biological nomenclature is required to be unambiguous, unique and stable. They criticise the Linnaean rank-based system of nomenclature for failing to satisfy such requirements for the naming of clades and species. To address this problem, the PhyloCode is proposed in recent years, in which three definitions for clade naming are given, i.e., the node-based, the stem-based, and the apomorphy-based. We are of the opinion that since the Linnaean binominal system of botanical nomenclature has existed for nearly 250 years, the rejection of this system and the adoption of the PhyloCode would create a state of chaos in botanical nomenclature. This does not mean that there exist no merits in the proposals made by the PhyloCode supporters. We suggest that further studies should be conducted for its practical application. (3) It has been well known that there are many problems with the application of the biological species concept in plants, and thus at the present time the majority of plant systematists actually seldom use this concept in their practical work. The rapid development of cladistic approach has motivated the proposal of the phylogenetic species concept. This species concept is established based on three criteria, i.e., the autamorphy, the diagnosability and the basal exclusivity, hence the autamorphy species concept, the diagnosability species concept, and the genealogical concept are created respectively. Nevertheless, the morpho-geographical species concept is still predominantly adopted in plant systematics. When using this species concept, however, we should also take into account the data from other sources, particularly those from pollination biology, breeding system and molecular systematics.     

A new and unified nomenclature for male fertility restorer (RF) proteins in higher plants

The male fertility restorer (RF) proteins belong to extended protein families associated with the cytoplasmic male sterility in higher plants. Up till now, there is no devised nomenclature for naming the RF proteins. The systematic sequencing of new plant species in recent years has uncovered the existence of several novel RF genes and their encoded proteins. Their naming has been simply arbitrary and could not be adequately handled in the context of comparative functional genomics. We propose in this study a unified nomenclature for the RF extended protein families across all plant species. This new and unified nomenclature relies upon previously developed nomenclature for the first ever characterized RF gene, RF2A/ALDH2B2, a member of ALDH gene superfamily, and adheres to the guidelines issued by the ALDH Genome Nomenclature Committees. The proposed nomenclature reveals that RF gene superfamily encodes currently members of 51 families. This unified nomenclature accommodates functional RF genes and pseudogenes, and offers the flexibility needed to incorporate additional RFs as they become available in future. In addition, we provide a phylogenetic relationship between the RF extended families and use computational protein modeling to demonstrate the high divergence of RF functional specializations through specific structural features of selected members of RF superfamily.     

聚乙二醇化重组人粒细胞刺激因子及其药品通用名称命名

有越来越多的聚乙二醇修饰人粒细胞刺激因子研发上市。为适应这类制品的发展,中国药品通用名命名原则也需要不断更新修订。简要介绍了聚乙二醇修饰蛋白技术以及WHO国际非专利药品名(INN)命名委员会对这类制品的命名情况,讨论了我国对这类制品的药品通用命名原则和方法,建议对聚乙二醇化不同的修饰形式在名称上适当加以区分,并注意加强与INN命名委员会的交流合作。     

27-Hydroxycholesterol,does it exist? On the nomenclature and stereochemistry of 26-hydroxylated sterols

Significant ambiguity exists in the scientific community with regard to the nomenclature of 26-hydroxylated oxysterols. Oxysterols constitute an important class of compounds that have biological roles in the regulation of cholesterol synthesis and as endogenous selective estrogen receptor modulators (SERMs). The ambiguity is attributable to deviations from clearly stated IUPAC rules and is likely to increase as more biologically active oxysterols are identified. This review provides a uniform approach to the naming of 26-hydroxylated sterols for those of current interest and for those on the horizon such as oxysterols of lanosterol that retain the unsaturation at C-24 and C-25 such as (E)-26-hydroxylanosterol. Using this molecule as a starting point, this review hopes to establish a common language to keep all investigators on the same page.