Coherent Nomenclature Research Articles

Evolution of T cell receptor beta loci in salmonids.

T-cell mediated immunity relies on a vast array of antigen specific T cell receptors (TR). Characterizing the structure of TR loci is essential to study the diversity and composition of T cell responses in vertebrate species. The lack of good-quality genome assemblies, and the difficulty to perform a reliably mapping of multiple highly similar TR sequences, have hindered the study of these loci in non-model organisms. High-quality genome assemblies are now available for the two main genera of Salmonids, Salmo and Oncorhynchus. We present here a full description and annotation of the TRB loci located on chromosomes 19 and 25 of rainbow trout (Oncorhynchus mykiss). To get insight about variations of the structure and composition of TRB locus across salmonids, we compared rainbow trout TRB loci with other salmonid species and confirmed that the basic structure of salmonid TRB locus is a double set of two TRBV-D-J-C loci in opposite orientation on two different chromosomes. Our data shed light on the evolution of TRB loci in Salmonids after their whole genome duplication (WGD). We established a coherent nomenclature of salmonid TRB loci based on comprehensive annotation. Our work provides a fundamental basis for monitoring salmonid T cell responses by TRB repertoire sequencing.

Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species.

Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima. Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha, U. decumbens and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands.

Distance measurements to quadrupolar nuclei: Evolution of the rotational echo double resonance technique.

Molecular structure determination is the basis for understanding chemical processes and the property of materials. The direct dependence of the magnetic dipolar interaction on the distance makes solid-state nuclear magnetic resonance (NMR) an excellent tool to study molecular structure when X-ray crystallography fails to provide atomic-resolution data. Although techniques to measure distances between pairs of isolated nuclear spin-1/2 pairs are routine and easy to implement using the rotational echo double resonance (REDOR) experiment (Gullion & Schaefer, 1989), the existence of a nucleus with a spin > 1/2, appearing in approximately 75% of the elements in the periodic table, poses a challenge due to difficulties stemming from the large nuclear quadrupolar coupling constant (QCC). This mini-review presents the existing solid-state magic-angle spinning NMR techniques aimed toward the efficient and accurate determination of internuclear distances between a spin-1/2 and a "quadrupolar" nucleus having a spin larger than one half. Analytical expressions are provided for the various recoupling curves stemming from different techniques, and a coherent nomenclature for these various techniques is suggested. Treatment of some special cases such as multiple spin effects and spins with close Larmor frequencies is also discussed. The most advanced methods can recouple spins with quadrupolar frequencies up to tens of megahertz and beyond, expanding the distance measurement capabilities of solid-state NMR to an increasingly growing number of applications and nuclear spin systems.

‘Cannabis’ ontologies I: Conceptual issues with Cannabis and cannabinoids terminology

Objective Identify a coherent nomenclature for Cannabis sativa L. derived products and their analogues. Design Research undertaken in parallel to the three-year assessment of Cannabis derivatives by the World Health Organisation. The scope is limited to Cannabis products intended for human incorporation (internal and topical consumption). Primarily embedded in pharmacognosy, the study incorporates a wide range of scholarly and grey literature, folk knowledge, archives, pharmacopœias, international law, field pharmacy, clinical and herbal medicine data, under a philosophical scrutiny. Generic and Cannabis-specific nomenclatural frames are compared to determine the extent to which they coincide or conflict. Results All lexica reviewed use weak, ambiguous, or inconsistent terms. There is insufficient scientific basis for terms and concepts related to Cannabis at all levels. No sound classification exists: current models conflict by adopting idiosyncratic, partial, outdated, or utilitarian schemes to arrange the extraordinarily numerous and diverse derivatives of the C. sativa plant. In law and policy, no clear or unequivocal boundary between herbal and non-herbal drugs, nor natural and synthetic cannabinoids was found; current nomenclatures need updates. In science, the botanical Cannabis lexicon overlooks parthenocarpy, and wide disagreement remains as to the taxonomy and systematics of the plant; chemical research should address differences in kinds between synthetic cannabinoids; pharmacopœias include little information related to Cannabis, and disagree on broader classes of herbal medicines, virtually failing to embrace many known Cannabis medicines. Since existing products and compounds fail to be categorised in an evidence-based manner, confusions will likely increase as novel cannabinoid compounds, genetic and biotechnological modifications surge. Conclusions The lack of clarity is comprehensive: for patients, physicians, and regulators. This study proposes an update of terms at several levels. It points at gaps in morphological descriptions in botany and pharmacognosy and a need for a metaphysical address of cannabinoids. Methods of obtention are identified as a common criterion to distinguish products; the way forward suggests a mutually exclusive nomenclatural pattern based on the smallest common denominator of obtention methods. In the context of a swelling number of Cannabis products being consumed (be it via medical prescription, adult-use, ‘hemp’ foodstuff and cosmetics, or other purposes), this study can assist research, contribute to transparent labelling of products, consumer safety and awareness, pharmacovigilance, medical standards of care, and an update of prevention and harm reduction approaches. It can also better inform regulatory policies surrounding C. sativa, its derivatives, and other cannabinoid-containing products.

Contributions to the taxonomy of the long-jawed orb-weaving spider genus Tetragnatha (Araneae, Tetragnathidae) in the Neotropical region, with comments on the morphology of the chelicerae

We newly diagnose, illustrate, and clarify the distribution ranges of six of the most common and broadly distributed species ofTetragnathaLatreille, 1804 found in the Neotropical region. Twenty new junior synonyms from around the world are included, nine forT. bogotensisKeyserling, 1865, four forT. mandibulataWalckenaer, 1841, three forT. keyserlingiSimon, 1890, three forT. nitens(Audouin, 1826), and one forT. elongataWalckenaer, 1841.Tetragnatha vermiformisEmerton, 1884 is newly recorded from South America. The ArgentineT. majorHolmberg, 1876 andT. ripariaHolmberg, 1876 are considered nomina dubia. Finally, we discuss the terminology of the structures of the chelicerae to establish a coherent nomenclature for teeth and fang cusps.

Biological CO2-Methanation: An Approach to Standardization

Power-to-Methane as one part of Power-to-Gas has been recognized globally as one of the key elements for the transition towards a sustainable energy system. While plants that produce methane catalytically have been in operation for a long time, biological methanation has just reached industrial pilot scale and near-term commercial application. The growing importance of the biological method is reflected by an increasing number of scientific articles describing novel approaches to improve this technology. However, these studies are difficult to compare because they lack a coherent nomenclature. In this article, we present a comprehensive set of parameters allowing the characterization and comparison of various biological methanation processes. To identify relevant parameters needed for a proper description of this technology, we summarized existing literature and defined system boundaries for Power-to-Methane process steps. On this basis, we derive system parameters providing information on the methanation system, its performance, the biology and cost aspects. As a result, three different standards are provided as a blueprint matrix for use in academia and industry applicable to both, biological and catalytic methanation. Hence, this review attempts to set the standards for a comprehensive description of biological and chemical methanation processes.

A proposal for coherent nomenclature of multicomponent crystals.

Here a new, systematic, unambiguous and unified nomenclature for multicomponent materials is presented. The approach simplifies naming schemes of extraordinary co-crystals containing multiple building blocks with different charges. Although the presented examples of cytosine compounds cannot cover all possibilities, they clearly show that the new nomenclature is flexible and can be easily extended to other multicomponent materials.

Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain.

H1 (or linker) histones are basic nuclear proteins that possess an evolutionarily conserved nucleosome-binding globular domain, GH1. They perform critical functions in determining the accessibility of chromatin DNA to trans-acting factors. In most metazoan species studied so far, linker histones are highly heterogenous, with numerous nonallelic variants cooccurring in the same cells. The phylogenetic relationships among these variants as well as their structural and functional properties have been relatively well established. This contrasts markedly with the rather limited knowledge concerning the phylogeny and structural and functional roles of an unusually diverse group of GH1-containing proteins in plants. The dearth of information and the lack of a coherent phylogeny-based nomenclature of these proteins can lead to misunderstandings regarding their identity and possible relationships, thereby hampering plant chromatin research. Based on published data and our in silico and high-throughput analyses, we propose a systematization and coherent nomenclature of GH1-containing proteins of Arabidopsis (Arabidopsis thaliana [L.] Heynh) that will be useful for both the identification and structural and functional characterization of homologous proteins from other plant species.

Selenoprotein Gene Nomenclature

The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4, and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine sulfoxide reductase B1), and SEPHS2 (selenophosphate synthetase 2). Selenoproteins without known functions have traditionally been denoted by SEL or SEP symbols. However, these symbols are sometimes ambiguous and conflict with the approved nomenclature for several other genes. Therefore, there is a need to implement a rational and coherent nomenclature system for selenoprotein-encoding genes. Our solution is to use the root symbol SELENO followed by a letter. This nomenclature applies to SELENOF (selenoprotein F, the 15-kDa selenoprotein, SEP15), SELENOH (selenoprotein H, SELH, C11orf31), SELENOI (selenoprotein I, SELI, EPT1), SELENOK (selenoprotein K, SELK), SELENOM (selenoprotein M, SELM), SELENON (selenoprotein N, SEPN1, SELN), SELENOO (selenoprotein O, SELO), SELENOP (selenoprotein P, SeP, SEPP1, SELP), SELENOS (selenoprotein S, SELS, SEPS1, VIMP), SELENOT (selenoprotein T, SELT), SELENOV (selenoprotein V, SELV), and SELENOW (selenoprotein W, SELW, SEPW1). This system, approved by the HUGO Gene Nomenclature Committee, also resolves conflicting, missing, and ambiguous designations for selenoprotein genes and is applicable to selenoproteins across vertebrates.

Towards a coherent nomenclature of plant viruses.

The International Committee on Taxonomy of Viruses (ICTV) has the decree to set the rules for the classification and naming of viruses. The species is the lowest level considered in the taxonomic hierarchy. In general, virus species are named according to the structure “ and the word ‘virus’”. A typical example is Tobacco mosaic virus [Genus: Tobamovirus]. With a few exceptions, this convention has been generally well accepted. As there is always room for improvement, virus nomenclature (King et al., 2011) can be managed more efficiently through several ways.

The observation of large semi-major axis Centaurs: Testing for the signature of a planetary-mass solar companion

Several objects whose perihelion lies between Jupiter and Neptune have large semi-major axes a>100au, two of them having semi-major axis above 1000au. Since these objects’ perihelia share the same region as the classical Centaurs, a coherent nomenclature for them could be large semi-major axis Centaurs (Laces). It has been argued that the classical Centaurs, with semi-major axes below 50au, originate from the Scattered Disk. However, the Laces most likely originate from the Oort Cloud. We determine the brightest object in the Laces, classical Centaurs (with semi-major axis >20au) and Scattered Disk populations using a procedure that introduces observational bias to a set of objects in orbits obtained from numerical simulations of the evolution of the Oort cloud and Scattered Disk in the framework of the Nice model. The application of the procedure consistently determines that the brightest distant Lace (semi-major axis above 500au) is fainter than the brightest classical Centaur by about one magnitude, no matter what parameters were used for the procedure. However, reality shows a reversed situation: there is an excess of Laces with lower visual magnitudes. It is not clear why this is the case. We test whether a planetary-mass solar companion could produce an excess of bright Laces in comparison with classical Centaurs. We find that with the companion there is an excess of luminous Laces compared to when there is no companion. However, the companion model also produces many classical Centaurs with lower visual magnitudes than the observed ones. Thus we conclude that the companion does not solve this visual magnitude inconsistency, although the results are in general more coherent under the model with the companion than without.

Toward conceptualization, discriminant validation, and coherent nomenclature for inter-disciplinary theoretical transfer.

Beyond calling attention to Lee, Cho, Seo, Lee, and Choi's (2014) worthy construct validation regimen, the purpose of this brief note is to extend the study's effect by interpreting the broader than usual empirical and theoretical connections in a way that may not be obvious.

Identification, immunogenicity, and cross-reactivity of type IV pilin and pilin-like proteins fromClostridium difficile

The Gram-positive anaerobe Clostridium difficile is the major cause of nosocomial diarrhea; manifestations of infection include diarrhea, pseudomembranous colitis, and death. Genes for type IV pili, a bacterial nanofiber often involved in colonization and until relatively recently described only in Gram-negatives, are present in all members of the Clostridiales. We hypothesized that any pilins encoded in the C. difficile genome would be immunogenic, as has been shown with pilins from Gram-negative organisms. We describe nine pilin or pilin-like protein genes, for which we introduce a coherent nomenclature, in the C. difficile R20291 genome. The nine predicted pilin or pilin-like proteins have relatively conserved N-terminal hydrophobic regions, but diverge at their C-termini. Analysis of synonymous and nonsynonymous substitutions revealed evidence of diversifying selective pressure in two pilin genes. Six of the nine identified proteins were purified and used to immunize mice. Immunization of mice with each individual protein generated antibody responses that varied in titer and cross-reactivity, a notable result given the low amino acid sequence identity among the pilins. Further studies in other small mammals mirrored our results in mice. Our results illuminate components of the C. difficile type IV pilus and help identify targets for an anti-C. difficile vaccine.

UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks

UCNEbase (http://ccg.vital-it.ch/UCNEbase) is a free, web-accessible information resource on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs). It currently covers 4351 such elements in 18 different species. The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes. As most of them occur as clusters near potential target genes, the database is organized along two hierarchical levels: individual UCNEs and ultra-conserved genomic regulatory blocks (UGRBs). UCNEbase introduces a coherent nomenclature for UCNEs reflecting their respective associations with likely target genes. Orthologous and paralogous UCNEs share components of their names and are systematically cross-linked. Detailed synteny maps between the human and other genomes are provided for all UGRBs. UCNEbase is managed by a relational database system and can be accessed by a variety of web-based query pages. As it relies on the UCSC genome browser as visualization platform, a large part of its data content is also available as browser viewable custom track files. UCNEbase is potentially useful to any computational, experimental or evolutionary biologist interested in conserved non-coding DNA elements in vertebrates.

Interdisciplinary approaches: towards new statistical methods for phenological studies

The importance of global environmental questions has significantly advanced the impact of climate change phenology. Whilst spatial applications continue to be a core application of phenology; in recent years the temporal dimension has also been revisited, with studies showing that temporal changes, either with a natural or an anthropogenic origin, have significantly altered phenological rhythms and seasonal development—changes attributed now to an anthropogenically induced temperature increase. This paper explores and introduces recent and newly developing analytic methods in phenology; with a view to increasing an interdisciplinary perspective and dialogue. Of particular focus is how we can and best deal with nonlinearity of phenological change in time and with multiple location studies; rigorously model the inherent multivariate time series structures in climate-phenology data; further Bayesian and non-Bayesian methods, detect multiple change-points; map seasonality calendars; model de-synchronisation of species globally; invoke old fashioned, yet rarely used circular statistical methods; adapt new transitional state modelling of phenophases with respect to climate and progress a unified paradigm for meta analytic studies in phenology. The provision of uncertainty analysis is also still much needed in climate-related phenological research. Reaching consensus on design, method of data collection and comparable analytic methods is integral to advancing the generalisability of phenological results; as is a consensus on inclusion criterion for studies selected for phenological meta-analytic studies. A coherent nomenclature is critically required, but it is currently lacking in many areas of phenology.

Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments

We present an expansion of the classification of the family Papillomaviridae, which now contains 29 genera formed by 189 papillomavirus (PV) types isolated from humans (120 types), non-human mammals, birds and reptiles (64, 3 and 2 types, respectively). To accommodate the number of PV genera exceeding the Greek alphabet, the prefix "dyo" is used, continuing after the Omega-PVs with Dyodelta-PVs. The current set of human PVs is contained within five genera, whereas mammalian, avian and reptile PVs are contained within 20, 3 and 1 genera, respectively. We propose standardizations to the names of a number of animal PVs. As prerequisite for a coherent nomenclature of animal PVs, we propose founding a reference center for animal PVs. We discuss that based on emerging species concepts derived from genome sequences, PV types could be promoted to the taxonomic level of species, but we do not recommend implementing this change at the current time.

ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes

Insertion sequences (ISs) are among the smallest and simplest autonomous transposable elements. ISfinder (http://www-is.biotoul.fr/) is a dedicated IS database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repository including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information (the complete nucleotide sequence, the sequence of the ends and target sites, potential open reading frames, strain of origin, distribution in other strains and available bibliography) and classified into a group or family to provide some insight into its phylogeny. ISfinder also includes extensive background information on ISs and transposons in general. Online tools are gradually being added. At present, it is difficult to visualize the global distribution of ISs in a given bacterial genome. Such information would facilitate understanding of the impact of these small transposable elements on shaping their host genome. Here we describe ISbrowser (http://www-genome.biotoul.fr/ISbrowser.php), an extension to the ISfinder platform and a tool which permits visualization of the position, orientation and distribution of complete and partial ISs in individual prokaryotic genomes.

SYMBOLS, SI UNITS AND PHYSICAL QUANTITIES WITHIN THE SCOPE OF SAP FLOW STUDIES

Some confusion was observed during the 7th International workshop on Sap Flow (Seville, Spain, 21-24 October 2008) with respect to the use of symbols, units and physical quantities in presentations and during discussions. It was therefore decided at the end of the workshop that a technical note would be very useful with the aim to summarize the basics of the “Systeme International des Unites (SI)” and to focus on particular aspects that are relevant for sap flow studies. Starting from a number of standard papers that have been published in the past, an extra effort was made to put sap flow nomenclature against the physical background of plant-water relationships, of water flow in the soil-plant-atmosphere continuum and of transport equations for mass, heat and hydraulic flow. Information is given on the application of SI units and the main SI conventions. Tables are included for practical use of basic and derived SI units and for common abbreviations encountered in sap flow studies. An overview of a coherent nomenclature for sap flow studies, together with definitions of sap flow quantities, symbols and units is given as well.

On the origin, homologies and evolution of primate facial muscles, with a particular focus on hominoids and a suggested unifying nomenclature for the facial muscles of the Mammalia.

The mammalian facial muscles are a subgroup of hyoid muscles (i.e. muscles innervated by cranial nerve VII). They are usually attached to freely movable skin and are responsible for facial expressions. In this study we provide an account of the origin, homologies and evolution of the primate facial muscles, based on dissections of various primate and non-primate taxa and a review of the literature. We provide data not previously reported, including photographs showing in detail the facial muscles of primates such as gibbons and orangutans. We show that the facial muscles usually present in strepsirhines are basically the same muscles that are present in non-primate mammals such as tree-shrews. The exceptions are that strepsirhines often have a muscle that is usually not differentiated in tree-shrews, the depressor supercilii, and lack two muscles that are usually differentiated in these mammals, the zygomatico-orbicularis and sphincter colli superficialis. Monkeys such as macaques usually lack two muscles that are often present in strepsirhines, the sphincter colli profundus and mandibulo-auricularis, but have some muscles that are usually absent as distinct structures in non-anthropoid primates, e.g. the levator labii superioris alaeque nasi, levator labii superioris, nasalis, depressor septi nasi, depressor anguli oris and depressor labii inferioris. In turn, macaques typically lack a risorius, auricularis anterior and temporoparietalis, which are found in hominoids such as humans, but have muscles that are usually not differentiated in members of some hominoid taxa, e.g. the platysma cervicale (usually not differentiated in orangutans, panins and humans) and auricularis posterior (usually not differentiated in orangutans). Based on our observations, comparisons and review of the literature, we propose a unifying, coherent nomenclature for the facial muscles of the Mammalia as a whole and provide a list of more than 300 synonyms that have been used in the literature to designate the facial muscles of primates and other mammals. A main advantage of this nomenclature is that it combines, and thus creates a bridge between, those names used by human anatomists and the names often employed in the literature dealing with non-human primates and non-primate mammals.

A Systematic Nomenclature for Codifying Engineered Nanostructures

Nanotechnology's growing applications are fueled by the synthesis and engineering of a myriad nanostructures, yet there is no systematic naming or classification scheme for such materials. This lack of a coherent nomenclature is confusing the interpretation of data sets and threatens to hamper the pace of progress and risk assessment. A systematic nomenclature that encodes the overall composition, size, shape, core and ligand chemistry, and solubility of nanostructures is presented. A typographic string of minimalist field codes facilitates digital archiving and searches for desired properties. This nomenclature system could also be used for nanomaterial hazard labeling.