Description and nomenclature of Neisseria meningitidis capsule locus

Pathogenic Neisseria meningitidis isolates contain a polysaccharide capsule that is the main virulence determinant for this bacterium. Thirteen capsular polysaccharides have been described, and nuclear magnetic resonance spectroscopy has enabled determination of the structure of capsular polysaccharides responsible for serogroup specificity. Molecular mechanisms involved in N. meningitidis capsule biosynthesis have also been identified, and genes involved in this process and in cell surface translocation are clustered at a single chromosomal locus termed cps. The use of multiple names for some of the genes involved in capsule synthesis, combined with the need for rapid diagnosis of serogroups commonly associated with invasive meningococcal disease, prompted a requirement for a consistent approach to the nomenclature of capsule genes. In this report, a comprehensive description of all N. meningitidis serogroups is provided, along with a proposed nomenclature, which was presented at the 2012 XVIIIth International Pathogenic Neisseria Conference.

Explanation and Use of the Colposcopy Terminology of the IFCPC (International Federation for Cervical Pathology and Colposcopy) Rio 2011

In July 2012 a revised terminology on colposcopic examinations of the cervix uteri was adopted by IFCPC. Central aspect is a description of characteristics that should aid in the definition of the disease entity cervix uteri. The nomenclature is built up in such a way that the examiner can evaluate colposcopic criteria according to a specific scheme. Firstly it is assessed whether the colposcopy is representative. Then it should be clarified whether or not the findings are normal. If the findings are not normal but rather abnormal the severity of the lesion is classified according to the so-called grade 1 (minor change) and grade 2 findings (major change). Specific abnormal findings such as leukoplakia, erosion and Lugol's finding are also not defined at this point. Characteristics suspicious for an invasion are described separately, in particular, atypical vessel patterns are mentioned here. As already held in the previous revised nomenclature (Barcelona), various findings are described in a last group: congenital transformation zones (CTZ), congenital anomalies, condylomas (papillomas), endometriosis, polyps (ectocervical, endocervical), inflammation, stenosis, postoperative changes (scarred portio, vaginal stump).

Identification, nomenclature, and evolutionary relationships of mitogen-activated protein kinase (MAPK) genes in soybean

Mitogen-activated protein kinase (MAPK) genes in eukaryotes regulate various developmental and physiological processes including those associated with biotic and abiotic stresses. Although MAPKs in some plant species including Arabidopsis have been identified, they are yet to be identified in soybean. Major objectives of this study were to identify GmMAPKs, assess their evolutionary relationships, and analyze their functional divergence. We identified a total of 38 MAPKs, eleven MAPKKs, and 150 MAPKKKs in soybean. Within the GmMAPK family, we also identified a new clade of six genes: four genes with TEY and two genes with TQY motifs requiring further investigation into possible legume-specific functions. The results indicated the expansion of the GmMAPK families attributable to the ancestral polyploidy events followed by chromosomal rearrangements. The GmMAPK and GmMAPKKK families were substantially larger than those in other plant species. The duplicated GmMAPK members presented complex evolutionary relationships and functional divergence when compared to their counterparts in Arabidopsis. We also highlighted existing nomenclatural issues, stressing the need for nomenclatural consistency. GmMAPK identification is vital to soybean crop improvement, and novel insights into the evolutionary relationships will enhance our understanding about plant genome evolution.

Taxonomy and phylogeny of European Gymnopus subsection Levipedes (Basidiomycota, Omphalotaceae)

The systematic integrity of European Gymnopus subsect. Levipedes is verified based on anatomic-morphological characters with support from DNA sequences of ITS and translation elongation factor 1-alpha genes. Seven species (G. alpinus, G. aquosus, G. dryophilus – including var. lanipes, G. erythropus, G. fagiphilus, G. hybridus, and G. ocior) belonging to this subsection are included. We clarify the concepts of G. dryophilus and G. ocior, which were occasionally confused in older literature. Due to unavailability of previously selected neotype of G. dryophilus the substitute neotype specimen is selected. Gymnopus dryophilus var. lanipes is confirmed as a variety; no important differences from nominotypical variability were detected. All discriminative characters used for identification of these species are discussed in detail. An identification key is also provided.

Respiratory system reactance is an independent determinant of asthma control

The mechanisms underlying not well-controlled (NWC) asthma remain poorly understood, but accumulating evidence points to peripheral airway dysfunction as a key contributor. The present study tests whether our recently described respiratory system reactance (Xrs) assessment of peripheral airway dysfunction reveals insight into poor asthma control. The aim of this study was to investigate the contribution of Xrs to asthma control. In 22 subjects with asthma, we measured Xrs (forced oscillation technique), spirometry, lung volumes, and ventilation heterogeneity (inert-gas washout), before and after bronchodilator administration. The relationship between Xrs and lung volume during a deflation maneuver yielded two parameters: the volume at which Xrs abruptly decreased (closing volume) and Xrs at this volume (Xrscrit). Lowered (more negative) Xrscrit reflects reduced apparent lung compliance at high lung volumes due, for example, to heterogeneous airway narrowing and unresolved airway closure or near closure above the critical lung volume. Asthma control was assessed via the 6-point Asthma Control Questionnaire (ACQ6). NWC asthma was defined as ACQ6 > 1.0. In 10 NWC and 12 well-controlled subjects, ACQ6 was strongly associated with postbronchodilator (post-BD) Xrscrit (R(2) = 0.43, P < 0.001), independent of all measured variables, and was a strong predictor of NWC asthma (receiver operator characteristic area = 0.94, P < 0.001). By contrast, Xrs measures at lower lung volumes were not associated with ACQ6. Xrscrit itself was significantly associated with measures of gas trapping and ventilation heterogeneity, thus confirming the link between Xrs and airway closure and heterogeneity. Residual airway dysfunction at high lung volumes assessed via Xrscrit is an independent contributor to asthma control.

Circumscription and lectotypification of Hedychium villosum and its variety H. villosum var. tenuiflorum (Zingiberaceae)

The nomenclatural confusion between the Indian gingers Hedychium villosum Wallich and its variety Hedychium villosum var. tenuiflorum (Wall. ex Voigt) Wall. ex Baker is discussed. Both taxa are lectotypified in order to stabilize the names and contribute towards a resolution of their confusing nomenclatural past. Both taxa are described in detail to aid identification.

Process-based expansion and neural differentiation of human pluripotent stem cells for transplantation and disease modeling

Robust strategies for developing patient-specific, human, induced pluripotent stem cell (iPSC)-based therapies of the brain require an ability to derive large numbers of highly defined neural cells. Recent progress in iPSC culture techniques includes partial-to-complete elimination of feeder layers, use of defined media, and single-cell passaging. However, these techniques still require embryoid body formation or coculture for differentiation into neural stem cells (NSCs). In addition, none of the published methodologies has employed all of the advances in a single culture system. Here we describe a reliable method for long-term, single-cell passaging of PSCs using a feeder-free, defined culture system that produces confluent, adherent PSCs that can be differentiated into NSCs. To provide a basis for robust quality control, we have devised a system of cellular nomenclature that describes an accurate genotype and phenotype of the cells at specific stages in the process. We demonstrate that this protocol allows for the efficient, large-scale, cGMP-compliant production of transplantable NSCs from all lines tested. We also show that NSCs generated from iPSCs produced with the process described are capable of forming both glia defined by their expression of S100β and neurons that fire repetitive action potentials.

DNA barcoding in Mucorales: an inventory of biodiversity

The order Mucorales comprises predominantly fast-growing saprotrophic fungi, some of which are used for the fermentation of foodstuffs but it also includes species known to cause infections in patients with severe immune or metabolic impairments. To inventory biodiversity in Mucorales ITS barcodes of 668 strains in 203 taxa were generated covering more than two thirds of the recognised species. Using the ITS sequences, Molecular Operational Taxonomic Units were defined by a similarity threshold of 99 %. An LSU sequence was generated for each unit as well. Analysis of the LSU sequences revealed that conventional phenotypic classifications of the Mucoraceae are highly artificial. The LSU- and ITS-based trees suggest that characters, such as rhizoids and sporangiola, traditionally used in mucoralean taxonomy are plesiomorphic traits. The ITS region turned out to be an appropriate barcoding marker in Mucorales. It could be sequenced directly in 82 % of the strains and its variability was sufficient to resolve most of the morphospecies. Molecular identification turned out to be problematic only for the species complexes of Mucor circinelloides, M. flavus, M. piriformis and Zygorhynchus moelleri. As many as 12 possibly undescribed species were detected. Intraspecific variability differed widely among mucorealean species ranging from 0 % in Backusella circina to 13.3 % in Cunninghamella echinulata. A high proportion of clinical strains was included for molecular identification. Clinical isolates of Cunninghamella elegans were identified molecularly for the first time. As a result of the phylogenetic analyses several taxonomic and nomenclatural changes became necessary. The genus Backusella was emended to include all species with transitorily recurved sporangiophores. Since this matched molecular data all Mucor species possessing this character were transferred to Backusella. The genus Zygorhynchus was shown to be polyphyletic based on ITS and LSU data. Consequently, Zygorhynchus was abandoned and all species were reclassified in Mucor. Our phylogenetic analyses showed, furthermore, that all non-thermophilic Rhizomucor species belong to Mucor. Accordingly, Rhizomucor endophyticus was transferred to Mucor and Rhizomucor chlamydosporus was synonymised with Mucor indicus. Lecto-, epi- or neotypes were designated for several taxa.

Elements of morphology: standard terminology for the external genitalia

An international group of clinicians working in the field of dysmorphology has initiated the standardization of terms used to describe human morphology. The goals are to standardize these terms and reach consensus regarding their definitions. In this way, we will increase the utility of descriptions of the human phenotype and facilitate reliable comparisons of findings among patients. Discussions with other workers in dysmorphology and related fields, such as developmental biology and molecular genetics, will become more precise. Here we introduce the anatomy of the male and female genitalia, and define and illustrate the terms that describe the major characteristics of these body regions. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

A synopsis of Harperocallis (Tofieldiaceae, Alismatales) with ten new combinations

Ten new combinations from Asagraea, Isidrogaliva, and Tofieldia are proposed in the previously monospecific genus Harperocallis (Tofieldiaceae, Alismatales). As circumscribed here, the genus is restricted to the Americas. The majority of species occur in the Andes or the Guayana region of northern South America; more than half have restricted distributions, and Harperocallis flava is narrowly endemic in the Coastal Plain of the southeastern United States. A key to species, synonymies, distributions, representative specimens, and salient notes are presented. Populations of the species are mapped and Harperocallis robustior is illustrated. A neotype is selected for Tofieldia frigida, here considered a synonym of Harperocallis falcata. Several recent records of Harperocallis longiflora, previously known only from the type collected in 1902, are reported.

The genera in the third catalogue (1836-1837) of Dejean's Coleoptera collection

All genus-group names first proposed or made available for the first time in the third edition of Dejean’s catalogue of his beetle collection are recorded. The following 18 names are made available for the first time in Dejean’s third catalogue: Batoscelis Dejean [Carabidae], Laphyra Dejean [Carabidae], Sauriodes Dejean [Staphylinidae], Abrobapta Dejean [Buprestidae], Selagis Dejean [Buprestidae], Eurhipis Dejean [Eucnemidae], Anaeretes Dejean [Scarabaeidae], Doryscelis Dejean [Scarabaeidae], Epilissus Dejean [Scarabaeidae], Hoploscelis Dejean [Scarabaeidae], Brachygenius Dejean [Tenebrionidae], Capnisa Dejean [Tenebrionidae], Heterocheira Dejean [Tenebrionidae], Selenomma Dejean [Tenebrionidae], Dactylocrepis Dejean [Curculionidae], Lophodes Dejean [Curculionidae], Heterarthron Dejean [Bostrichidae] and Homalopus Chevrolat [Chrysomelidae]. Eurhipis Dejean, 1836 is considered a junior synonym of Phyllocerus Lepeletier and Audinet-Serville, 1825 for the first time. Abrobapta Dejean, 1836 has precedence over Torresita Harold, 1869.

Shorthand notation for lipid structures derived from mass spectrometry

There is a need for a standardized, practical annotation for structures of lipid species derived from mass spectrometric approaches; i.e., for high-throughput data obtained from instruments operating in either high- or low-resolution modes. This proposal is based on common, officially accepted terms and builds upon the LIPID MAPS terminology. It aims to add defined levels of information below the LIPID MAPS nomenclature, as detailed chemical structures, including stereochemistry, are usually not automatically provided by mass spectrometric analysis. To this end, rules for lipid species annotation were developed that reflect the structural information derived from the analysis. For example, commonly used head group-specific analysis of glycerophospholipids (GP) by low-resolution instruments is neither capable of differentiating the fatty acids linked to the glycerol backbone nor able to define their bond type (ester, alkyl-, or alk-1-enyl-ether). This and other missing structural information is covered by the proposed shorthand notation presented here. Beyond GPs, we provide shorthand notation for fatty acids/acyls (FA), glycerolipids (GL), sphingolipids (SP), and sterols (ST). In summary, this defined shorthand nomenclature provides a standard methodology for reporting lipid species from mass spectrometric analysis and for constructing databases.

The genera in the second catalogue (1833-1836) of Dejean's Coleoptera collection

All genus-group names listed in the second edition of the catalogue (1833-1836) of Dejean’s beetle collection are recorded. For each new genus-group name the originally included available species are listed and for generic names with at least one available species, the type species and the current status are given. Names available prior to the publication of Dejean’s second catalogue (1833-1836) are listed in an appendix.

The following new synonymies are proposed: Cyclonotum Dejean, 1833 (= Dactylosternum Wollaston, 1854) [Hydrophilidae], Hyporhiza Dejean, 1833 (= Rhinaspis Perty, 1830) [Scarabaeidae], Aethales Dejean, 1834 (= Epitragus Latreille, 1802) [Tenebrionidae], Arctylus Dejean, 1834 (= Praocis Eschscholtz, 1829) [Tenebrionidae], Euphron Dejean, 1834 (= Derosphaerus Thomson, 1858) [Tenebrionidae], Hipomelus Dejean, 1834 (= Trachynotus Latreille, 1828) [Tenebrionidae], Pezodontus Dejean, 1834 (= Odontopezus Alluaud, 1889) [Tenebrionidae], Zygocera Dejean, 1835 (= Disternopsis Breuning, 1939) [Cerambycidae], and Physonota Chevrolat, 1836 (= Anacassis Spaeth, 1913) [Chrysomelidae]. Heterogaster pilicornis Dejean, 1835 [Cerambycidae] and Labidomera trimaculata Chevrolat, 1836 [Chrysomelidae] are placed for the first time in synonymy with Anisogaster flavicans Deyrolle, 1862 and Chrysomela clivicollis Kirby, 1837 respectively. Type species of the following genus-group taxa are proposed: Sphaeromorphus Dejean, 1833 (Sphaeromorphus humeralis Erichson, 1843) [Scarabaeidae], Adelphus Dejean, 1834 (Helops marginatus Fabricius, 1792) [Tenebrionidae], Cyrtoderes Dejean, 1834 (Tenebrio cristatus DeGeer, 1778) [Tenebrionidae], Selenepistoma Dejean, 1834 (Opatrum acutum Wiedemann, 1823) [Tenebrionidae], Charactus Dejean, 1833 (Lycus limbatus Fabricius, 1801) [Lycidae], Corynomalus Chevrolat, 1836 (Eumorphus limbatus Olivier, 1808) [Endomychidae], Hebecerus Dejean, 1835 (Acanthocinus marginicollis Boisduval, 1835) [Cerambycidae], Pterostenus Dejean, 1835 (Cerambyx abbreviatus Fabricius, 1801) [Cerambycidae], Psalicerus Dejean, 1833 (Lucanus femoratus Fabricius, 1775) [Lucanidae], and Pygolampis Dejean, 1833 (Lampyris glauca Olivier, 1790) [Lampyridae]. A new name, Neoeutrapela Bousquet and Bouchard [Tenebrionidae], is proposed for Eutrapela Dejean, 1834 (junior homonym of Eutrapela Hübner, 1809).

The following generic names, made available in Dejean’s catalogue, were found to be older than currently accepted valid names: Catoxantha Dejean, 1833 over Catoxantha Solier, 1833 [Buprestidae], Pristiptera Dejean, 1833 over Pelecopselaphus Solier, 1833 [Buprestidae], Charactus Dejean, 1833 over Calopteron Laporte, 1836 [Lycidae], Cyclonotum Dejean, 1833 over Dactylosternum Wollaston, 1854 [Hydrophilidae], Ancylonycha Dejean, 1833 over Holotrichia Hope, 1837 [Scarabaeidae], Aulacium Dejean, 1833 over Mentophilus Laporte, 1840 [Scarabaeidae], Sciuropus Dejean, 1833 over Ancistrosoma Curtis, 1835 [Scarabaeidae], Sphaeromorphus Dejean, 1833 over Ceratocanthus White, 1842 [Scarabaeidae], Psalicerus Dejean, 1833 over Leptinopterus Hope, 1838 [Lucanidae], Adelphus Dejean, 1834 over Praeugena Laporte, 1840 [Tenebrionidae], Amatodes Dejean, 1834 over Oncosoma Westwood, 1843 [Tenebrionidae], Cyrtoderes Dejean, 1834 over Phligra Laporte, 1840 [Tenebrionidae], Euphron Dejean, 1834 over Derosphaerus Thomson, 1858 [Tenebrionidae], Pezodontus Dejean, 1834 over Odontopezus Alluaud, 1889 [Tenebrionidae], Anoplosthaeta Dejean, 1835 over Prosopocera Blanchard, 1845 [Cerambycidae], Closteromerus Dejean, 1835 over Hylomela Gahan, 1904 [Cerambycidae], Hebecerus Dejean, 1835 over Ancita Thomson, 1864 [Cerambycidae], Mastigocera Dejean, 1835over Mallonia Thomson, 1857 [Cerambycidae], Zygocera Dejean, 1835 over Disternopsis Breuning, 1939 [Cerambycidae], Australica Chevrolat, 1836 over Calomela Hope, 1840 [Chrysomelidae], Edusa Chevrolat, 1836 over Edusella Chapuis, 1874 [Chrysomelidae], Litosonycha Chevrolat, 1836 over Asphaera Duponchel and Chevrolat, 1842 [Chrysomelidae], and Pleuraulaca Chevrolat, 1836 over Iphimeis Baly, 1864 [Chrysomelidae]. In each of these cases, Reversal of Precedence (ICZN 1999: 23.9) or an applicationto the International Commission on Zoological Nomenclature will be necessary to retain usage of the younger synonyms.

In silico tissue-distribution of human Rho family GTPase activating proteins

Rho family small GTPases are involved in the spatio-temporal regulation of several physiological processes. They operate as molecular switches based on their GTP- or GDP-bound state. Their GTPase activator proteins (Rho/Rac GAPs) are able to increase the GTP hydrolysis of small GTPases, which turns them to an inactive state. This regulatory step is a key element of signal termination. According to the human genome project the potential number of Rho family GAPs is approximately 70. Despite their significant role in cellular signaling our knowledge on their expression pattern is quite incomplete. In this study we tried to reveal the tissue-distribution of Rho/Rac GAPs based on expressed sequence tag (EST) database from healthy and tumor tissues and microarray experiments. Our accumulated data sets can provide important starting information for future research. However, the nomenclature of Rho family GAPs is quite heterogeneous. Therefore we collected the available names, abbreviations and aliases of human Rho/Rac GAPs in a useful nomenclature table. A phylogenetic tree and domain structure of 65 human RhoGAPs are also presented.

Decoding laboratory test names: a major challenge to appropriate patient care

Clinical laboratory tests have no value if clinicians cannot quickly order and obtain the results they need. We found that efforts to obtain even the most commonly ordered tests are often derailed by excessively complex nomenclature. Ordering the right laboratory tests is critical to diagnosis and treatment, but existing mechanisms for entering lab orders actively interfere with physicians' efforts to provide good clinical care. Rather than simplifying lab orders, the advent of computerized physician order entry (CPOE) systems-generally programmed by non-clinicians-has introduced new and vexing practical problems. Medical laboratories have filled their test menus, whether paper or electronic, with bewildering nomenclature and abbreviations, and have failed to appreciate the dangers of assigning perilously similar names to different tests. The efficient and efficacious patient care demanded by the quality care initiative requires progress beyond traditional solutions, such as convening naming conventions, to the development of innovative software with intelligent, real-time, clinically driven search functions that will allow these programs to help rather than hinder physicians.

Alternative splicing in the aldo-keto reductase superfamily: implications for protein nomenclature

The aldo-keto reductase superfamily contains 173 proteins which are present in all phyla. Examination of the human and mouse genomes has identified that in some instances a single AKR gene can give rise to alternatively spliced mRNA variants which in some cases can give rise to more than one protein isoform. This is currently well documented in the AKR6A subfamily which contains the β-subunits of the voltage-gated potassium ion channels. With the emergence of second generation sequencing it is likely that the occurrence of transcript variants and protein isoforms from a single AKR gene may become common place. To deal with this issue we recommend that the Ensembl data-base nomenclature be used to annotate the transcript variants from a single AKR gene. However, since multiple transcript variants could give rise to either the same or multiple protein isoforms from the same AKR gene we also propose to expand the nomenclature of the AKR protein superfamily, so that when a protein isoform is shown to be expressed and is functional it would be assigned the standard AKR name followed by a "period or full-stop" and a number for that unique isoform. Numbers will be assigned chronologically and linked to the respective transcripts annotated in Ensembl e.g. AKR6A5.1 (Kvβ2.1) (AKR6A5-001, -006 and -201), followed by AKR6A5.2 (Kvβ2.2) (AKR6A5-002,-202). This nomenclature is expandable and it enables multiple protein isoforms to be assigned to their respective transcripts when they arise from the same AKR gene or for a single protein isoform to be assigned to multiple transcripts when the transcripts encode the same AKR protein.

A revised circumscription for the Blakeeae (Melastomataceae) with associated nomenclatural adjustments

Systematic investigations and phylogenetic analyses of the Blakeeae (Melastomataceae) have indicated that Topobea should be synonymized under Blakea, and Huilaea under Chalybea. Presented here is a detailed description of the Blakeeae, a key to its two accepted genera, and a listing of 62 new combinations, including 3 new names, necessitated by the transfer of Topobea as follows: Blakea acuminata (Wurdack) Penneys & Judd, comb. nov., Blakea adscendens (E.Cotton & Matezki) Penneys & Judd, comb. nov., Blakea albertiae (Wurdack) Penneys & Almeda, comb. nov., Blakea amplifolia (Almeda) Penneys & Almeda, comb. nov., Blakea arboricola (Almeda) Penneys & Almeda, comb. nov., Blakea asplundii (Wurdack) Penneys & Judd, comb. nov., Blakea barbata (Gleason) Penneys & Judd, comb. nov., Blakea brenesii (Standl.) Penneys & Almeda, comb. nov., Blakea brevibractea (Gleason) Penneys & Judd, comb. nov., Blakea bullata (E.Cotton & Matezki) Penneys & Judd, comb. nov., Blakea calcarata (L.Uribe) Penneys & Judd, comb. nov., Blakea calophylla (Almeda) Penneys & Almeda, comb. nov., Blakea calycularis (Naudin) Penneys & Almeda, comb. nov., Blakea castanedae (Wurdack) Penneys & Judd, comb. nov., Blakea clavata (Triana) Penneys & Judd, nom. nov., Blakea cordata (Gleason) Penneys & Almeda, comb. nov., Blakea cuprina Penneys & Judd, nom. nov., Blakea cutucuensis (Wurdack) Penneys & Judd, comb. nov., Blakea dimorphophylla (Almeda) Penneys & Almeda, comb. nov., Blakea discolor (Hochr.) Penneys & Judd, comb. nov., Blakea dodsonorum (Wurdack) Penneys & Almeda, comb. nov., Blakea eplingii (Wurdack) Penneys & Judd, comb. nov., Blakea ferruginea (Gleason) Penneys & Judd, comb. nov., Blakea fragrantissima (Almeda) Penneys & Almeda, comb. nov., Blakea gerardoana (Almeda) Penneys & Almeda, comb. nov., Blakea glaberrima (Triana) Penneys & Judd, comb. nov., Blakea henripittieri (Cogn.) Penneys & Almeda, comb. et nom. nov., Blakea hexandra (Almeda) Penneys & Almeda, comb. nov., Blakea horologica Penneys & Judd, nom. nov., Blakea induta (Markgr.) Penneys & Judd, comb. nov., Blakea inflata (Triana) Penneys & Judd, comb. nov., Blakea insignis (Triana) Penneys & Judd, comb. nov., Blakea intricata (Almeda) Penneys & Almeda, comb. nov., Blakea killipii (Wurdack) Penneys & Judd, comb. nov., Blakea lentii (Almeda) Penneys & Almeda, comb. nov., Blakea longiloba (Wurdack) Penneys & Judd, comb. nov., Blakea longisepala (Gleason) Penneys & Judd, comb. nov., Blakea macbrydei (Wurdack) Penneys & Judd, comb. nov., Blakea maguirei (Wurdack) Penneys & Judd, comb. nov., Blakea maurofernandeziana (Cogn.) Penneys & Almeda, comb. nov., Blakea mcphersonii (Almeda) Penneys & Almeda, comb. nov., Blakea modica (Wurdack) Penneys & Judd, comb. nov., Blakea mortoniana (Wurdack) Penneys & Judd, comb. nov., Blakea muricata (Lozano) Penneys & Judd, comb. nov., Blakea pascoensis (Wurdack) Penneys & Judd, comb. nov., Blakea pluvialis (Standl.) Penneys & Almeda, comb. nov., Blakea sessilifolia (Triana) Penneys & Judd, comb. nov., Blakea setosa (Triana) Penneys & Judd, comb. nov., Blakea standleyi (L.O.Williams) Penneys & Almeda, comb. nov., Blakea stephanochaeta (Naudin) Penneys & Judd, comb. nov., Blakea steyermarkii (Wurdack) Penneys & Judd, comb. nov., Blakea suaveolens (Almeda) Penneys & Almeda, comb. nov., Blakea subbarbata (Wurdack) Penneys & Judd, comb. nov., Blakea subscabrula (Triana) Penneys & Judd, comb. nov., Blakea subsessiliflora (Wurdack) Penneys & Judd, comb. nov., Blakea superba (Naudin) Penneys & Judd, comb. nov., Blakea tetramera (Almeda) Penneys & Almeda, comb. nov., Blakea tetroici (Wurdack) Penneys & Judd, comb. nov., Blakea toachiensis (Wurdack) Penneys & Judd, comb. nov., Blakea trianae (Cogn.) Penneys & Judd, comb. nov., Blakea verrucosa (Wurdack) Penneys & Judd, comb. nov., Blakea watsonii (Cogn.) Penneys & Almeda, comb. nov.

Complex regional pain syndrome acceptance and the alternative denominations in the medical literature

OBJECTIVE

To analyze the use of the term 'complex regional pain syndrome' in the medical literature and evaluate whether or not the traditional names 'reflex sympathetic dystrophy' and 'causalgia' have already been replaced with the new terms 'complex regional pain syndrome type I' and 'complex regional pain syndrome type II', respectively.

MATERIALS AND METHODS

The Scopus and PubMed databases were searched for reports written between 2001 and 2012 for the following descriptors in the titles: 'complex regional pain syndrome', 'complex regional pain syndrome type I', 'complex regional pain syndrome type 1', 'complex regional pain syndrome type II', 'complex regional pain syndrome type 2', 'CRPS', 'CRPS type I', 'CRPS type 1', 'CRPS type II', 'CRPS type 2', 'reflex sympathetic dystrophy', 'algodystrophy', 'algoneurodystrophy', 'causalgia', 'transient osteoporosis', 'Sudeck', and 'shoulder-hand syndrome'.

RESULTS

Systematization of the 1,318 articles found yielded the following: 953 (72.31%) articles for the descriptor 'complex regional pain syndrome' and a further 94 (7.13%) for its abbreviation 'CRPS'; 180 (13.66%) for 'reflex sympathetic dystrophy'; 33 (2.50%) for 'shoulder-hand syndrome'; 29 (2.20%) for 'algodystrophy'; 13 (0.99%) for 'causalgia'; 13 (0.99%) for 'Sudeck'; 2 (0.15%) for 'algoneurodystrophy', and 1 (0.08%) for 'transient osteoporosis'. The total number of articles using new terminology represents 1,047 (79.44%) of all articles.

CONCLUSION

The new neutral term 'complex regional pain syndrome' was most commonly used and will likely replace the traditional names 'reflex sympathetic dystrophy' and 'causalgia'. The new terminology is now widely accepted by the medical professionals who are mostly engaged in the treatment of CRPS patients, but not yet so in other medical spheres.

Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

In recent years, there has been a significant increase in the number of completely sequenced plant genomes. The comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. The aldehyde dehydrogenase (ALDH) gene superfamily comprises a group of enzymes involved in the NAD(+)- or NADP(+)-dependent conversion of various aldehydes to their corresponding carboxylic acids. ALDH enzymes are involved in processing many aldehydes that serve as biogenic intermediates in a wide range of metabolic pathways. In addition, many of these enzymes function as 'aldehyde scavengers' by removing reactive aldehydes generated during the oxidative degradation of lipid membranes, also known as lipid peroxidation. Plants and animals share many ALDH families, and many genes are highly conserved between these two evolutionarily distinct groups. Conversely, both plants and animals also contain unique ALDH genes and families. Herein we carried out genome-wide identification of ALDH genes in a number of plant species-including Arabidopsis thaliana (thale crest), Chlamydomonas reinhardtii (unicellular algae), Oryza sativa (rice), Physcomitrella patens (moss), Vitis vinifera (grapevine) and Zea mays (maize). These data were then combined with previous analysis of Populus trichocarpa (poplar tree), Selaginella moellindorffii (gemmiferous spikemoss), Sorghum bicolor (sorghum) and Volvox carteri (colonial algae) for a comprehensive evolutionary comparison of the plant ALDH superfamily. As a result, newly identified genes can be more easily analyzed and gene names can be assigned according to current nomenclature guidelines; our goal is to clarify previously confusing and conflicting names and classifications that might confound results and prevent accurate comparisons between studies.

A taxonomic review of Attevidae (Lepidoptera: Yponomeutoidea) from China with descriptions of two new species and a revised identity of the Ailanthus webworm moth, Atteva fabriciella, from the Asian tropics

This review describes four species of Atteva (Lepidoptera: Yponomeutoidea: Attevidae) from China, including two new species: A. wallengreni n. sp. and A. yanguifella n. sp. The taxonomic identity of the Ailanthus webworm moth from South and Southeast Asia is revised with a designation of neotype for Phalaena (Tinea) fabriciella Swederus. Lectotypes of Atteva brucea Moore and A. niviguttella Walker are designated. Atteva brucea is synonymized with A. fabriciella. Synonymy of Atteva niviguttella and A. fabriciella is reconfirmed. The previous Chinese records of A. fabriciella were based on confusions with A. wallengreni n. sp. Confirmed specimens of A. fabriciella from China are reported. A pair of confused species, A. fabriciella and A. wallengreni n. sp., are distinguished by the number of white dots on the forewings and the genital features. Another confused pair, A. niveigutta and A. yanguifella n. sp., are compared by external and genital features. All type specimens of the described species are illustrated and compared with the conspecific specimens from various countries of the Asian tropics. Keys to all the species from China are provided.

Proliferative and non-proliferative lesions of the rat and mouse integument

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) project is a joint initiative of the societies of toxicological pathology from Europe (ESTP), Great Britain (BSTP), Japan (JSTP) and North America (STP). Its aim is to develop an internationally-accepted nomenclature for proliferative and non-proliferative lesions in laboratory rodents. A widely accepted international harmonization of nomenclature in laboratory animals will decrease confusion among regulatory and scientific research organizations in different countries and will provide a common language to increase and enrich international exchanges of information among toxicologists and pathologists. The purpose of this publication is to provide a standardized nomenclature for classifying microscopical lesions observed in the integument of laboratory rats and mice. Example colour images are provided for most lesions. The standardized nomenclature presented in this document and additional colour images are also available electronically at http://www.goreni.org. The nomenclature presented herein is based on histopathology databases from government, academia, and industrial laboratories throughout the world, and covers lesions that develop spontaneously as well as those induced by exposure to various test materials. (DOI: 10.1293/tox.26.27S; J Toxicol Pathol 2013; 26: 27S-57S).

Toward a monophyletic Cheilanthes: The resurrection and recircumscription of Myriopteris (Pteridaceae)

The fern genus Cheilanthes (Pteridaceae) has perplexed taxonomists for more than two centuries. Complex patterns of evolution involving rampant morphological convergence, polyploidy, hybridization, and apomixis have made the taxonomy of this group especially difficult. Fortunately, recent phylogenetic analyses have helped to clarify relationships among cheilanthoid taxa. Based on these findings, we here formalize an updated taxonomy for one monophyletic clade comprising 47 primarily North and Central American taxa usually included in Cheilanthes. Because the type species of Cheilanthes (Cheilanthes micropteris) is only distantly related to this clade, we resurrect the genus Myriopteris to accommodate these taxa, and present a revised circumscription for the group, including 36 new combinations.

Clarifications needed concerning the new Article 59 dealing with pleomorphic fungi

The new rules formulated in Article 59 of the International Code of Nomenclature for algae, fungi, and plants (ICN) will cause numerous, often undesirable, name changes, when only phylogenetically defined clades are named. Our task is to name fungal taxa and not just clades. Two suggestions are made here that may help to alleviate some disadvantages of the new system. (1) Officially an epithet coined in a list-demoted genus that is older than the oldest one available in the list-accepted genus would have to be recombined in the accepted genus. We recommend that individual authors and committees establishing lists of protected names should generally not recombine older epithets from a demoted genus into the accepted genus, when another one from pre-2013 is available in that genus. (2) Because the concepts of correlated teleomorph and anamorph genera are often incongruent, enforced congruence leads to a loss of information. Retaining the most suitable generic name is imperative, even when this is subordinated to another, list-accepted, generic name. Some kind of cryptic dual generic nomenclature is bound to persist. We therefore strongly recommend the retention of binomials in genera where they are most informative. With these recommendations, the upheaval of fungal nomenclature ensuing from the loss of the former Art. 59 can be reduced to an unavoidable minimum.

Addressing the conundrum of unavailable name-bearing types

Access to name-bearing type material can be a particular frustration for those mycologists in the tropics, or working outside established institutions, where the specimens are known to exist but cannot be examined. They can be inaccessible because of loans policies and the inability of mycologists to make personal visits. Each case has to be considered separately, but a pragmatic nine-point approach is presented which may provide some guidance as to what can be done in such instances. A postscript draws attention to 12 points to consider when designated or handling name-bearing types.

Reappraisal and neotypification of Phyllachora feijoae

Acca sellowiana (Myrtaceae), feijoa (in Brazil, goiaba da serra), is a native southern South America tree that produces edible fruits which, although only occasionally cultivated in South America, became a significant fruit crop in New Zealand. Recently, during surveys for fungal pathogens of feijoa in southern Brazil, several plants were found bearing tar-spot symptoms caused by a species of Phyllachora. A literature search enabled us to identify the fungus as Phyllachora feijoae, a little-known species originally described in the 19^th century by H. Rehm and later transferred to the genus Catacauma. The name Catacauma feijoae, although now regarded as a later synonym of P. feijoae is still mistakenly in use (as, for instance, in the Brazilian list of fungi on plants). The type specimen was most probably deposited in the Botanisches Garten und Museum Berlin-Dahlem (B) and lost or destroyed during World War II, and could not be located. The recent recollection of abundant material of this fungus in the vicinity of Pelotas (Rio Grande do Sul, Brazil) allowed its re-examination and neotypification. Phyllachora feijoae is also illustrated here for the first time.

A novel abbreviation standard for organobromine, organochlorine and organophosphorus flame retardants and some characteristics of the chemicals

Ever since the interest in organic environmental contaminants first emerged 50years ago, there has been a need to present discussion of such chemicals and their transformation products using simple abbreviations so as to avoid the repetitive use of long chemical names. As the number of chemicals of concern has increased, the number of abbreviations has also increased dramatically, sometimes resulting in the use of different abbreviations for the same chemical. In this article, we propose abbreviations for flame retardants (FRs) substituted with bromine or chlorine atoms or including a functional group containing phosphorus, i.e. BFRs, CFRs and PFRs, respectively. Due to the large number of halogenated and organophosphorus FRs, it has become increasingly important to develop a strategy for abbreviating the chemical names of FRs. In this paper, a two step procedure is proposed for deriving practical abbreviations (PRABs) for the chemicals discussed. In the first step, structural abbreviations (STABs) are developed using specific STAB criteria based on the FR structure. However, since several of the derived STABs are complicated and long, we propose instead the use of PRABs. These are, commonly, an extract of the most essential part of the STAB, while also considering abbreviations previously used in the literature. We indicate how these can be used to develop an abbreviation that can be generally accepted by scientists and other professionals involved in FR related work. Tables with PRABs and STABs for BFRs, CFRs and PFRs are presented, including CAS (Chemical Abstract Service) numbers, notes of abbreviations that have been used previously, CA (Chemical Abstract) name, common names and trade names, as well as some fundamental physico-chemical constants.

A revision of the Megachile subgenus Litomegachile Mitchell with an illustrated key and description of a new species (Hymenoptera, Megachilidae, Megachilini)

The species of Megachile subgenus Litomegachile are revised with a review of the species morphology, biology, and plant associations. A new species, Megachile pankus, is described and illustrated. Megachile mendica snowi Mitchell is elevated to species. Megachile var. nupta Cresson and Megachile texana var. cleomis Cockerell are synonymized with Megachile brevis and Megachile texana, respectively. An illustrated key for Litomegachile is also provided.

Phylogeny of Penicillium and the segregation of Trichocomaceae into three families

Species of Trichocomaceae occur commonly and are important to both industry and medicine. They are associated with food spoilage and mycotoxin production and can occur in the indoor environment, causing health hazards by the formation of β-glucans, mycotoxins and surface proteins. Some species are opportunistic pathogens, while others are exploited in biotechnology for the production of enzymes, antibiotics and other products. Penicillium belongs phylogenetically to Trichocomaceae and more than 250 species are currently accepted in this genus. In this study, we investigated the relationship of Penicillium to other genera of Trichocomaceae and studied in detail the phylogeny of the genus itself. In order to study these relationships, partial RPB1, RPB2 (RNA polymerase II genes), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences were obtained. The Trichocomaceae are divided in three separate families: Aspergillaceae, Thermoascaceae and Trichocomaceae. The Aspergillaceae are characterised by the formation flask-shaped or cylindrical phialides, asci produced inside cleistothecia or surrounded by Hülle cells and mainly ascospores with a furrow or slit, while the Trichocomaceae are defined by the formation of lanceolate phialides, asci borne within a tuft or layer of loose hyphae and ascospores lacking a slit. Thermoascus and Paecilomyces, both members of Thermoascaceae, also form ascospores lacking a furrow or slit, but are differentiated from Trichocomaceae by the production of asci from croziers and their thermotolerant or thermophilic nature. Phylogenetic analysis shows that Penicillium is polyphyletic. The genus is re-defined and a monophyletic genus for both anamorphs and teleomorphs is created (Penicillium sensu stricto). The genera Thysanophora, Eupenicillium, Chromocleista, Hemicarpenteles and Torulomyces belong in Penicilliums. str. and new combinations for the species belonging to these genera are proposed. Analysis of Penicillium below genus rank revealed the presence of 25 clades. A new classification system including both anamorph and teleomorph species is proposed and these 25 clades are treated here as sections. An overview of species belonging to each section is presented.

Nomenclatural benchmarking: the roles of digital typification and telemicroscopy

Nomenclatural benchmarking is the periodic realignment of species names with species theories and is necessary for the accurate and uniform use of Linnaean binominals in the face of changing species limits. Gaining access to types, often for little more than a cursory examination by an expert, is a major bottleneck in the advance and availability of biodiversity informatics. For the nearly two million described species it has been estimated that five to six million name-bearing type specimens exist, including those for synonymized binominals. Recognizing that examination of types in person will remain necessary in special cases, we propose a four-part strategy for opening access to types that relies heavily on digitization and that would eliminate much of the bottleneck: (1) modify codes of nomenclature to create registries of nomenclatural acts, such as the proposed ZooBank, that include a requirement for digital representations (e-types) for all newly described species to avoid adding to backlog; (2) an "r" strategy that would engineer and deploy a network of automated instruments capable of rapidly creating 3-D images of type specimens not requiring participation of taxon experts; (3) a "K" strategy using remotely operable microscopes to engage taxon experts in targeting and annotating informative characters of types to supplement and extend information content of rapidly acquired e-types, a process that can be done on an as-needed basis as in the normal course of revisionary taxonomy; and (4) creation of a global e-type archive associated with the commissions on nomenclature and species registries providing one-stop-shopping for e-types. We describe a first generation implementation of the "K" strategy that adapts current technology to create a network of Remotely Operable Benchmarkers Of Types (ROBOT) specifically engineered to handle the largest backlog of types, pinned insect specimens. The three initial instruments will be in the Smithsonian Institution(Washington, DC), Natural History Museum (London), and Museum National d'Histoire Naturelle (Paris), networking the three largest insect collections in the world with entomologists worldwide. These three instruments make possible remote examination, manipulation, and photography of types for more than 600,000 species. This is a cybertaxonomy demonstration project that we anticipate will lead to similar instruments for a wide range of museum specimens and objects as well as revolutionary changes in collaborative taxonomy and formal and public taxonomic education.

Managing and coping with names of pleomorphic fungi in a period of transition

An explanation is provided of the recent changes in the International Code of Nomenclature for algae, fungi and plants relating to the ending of the separate naming of different states of fungi with a pleomorphic life-cycle. Issues relating to their implementation are discussed, including problems of defining "widely used", author citations, proofs of holomorphy, typification, the preparation of "Lists of accepted and rejected names" (with a possible timetable), relationship to the existing processes of sanctioning and conservation or rejection, and steps to be considered for the future. This material is presented here to stimulate debate on the actions that should be taken by individuals, and responsible committees, in the current period of transition to a system of fungal nomenclature fit for the 21(st) century.

Taxonomic novelties in Scapania

Five new supraspecific taxa of Scapania are proposed, Scapania subg. Gracilidae, Scapania subg. Pseudomacrodiplophyllum, Scapania sect. Americanae, Scapania sect. Hyperboreae, and Scapania sect. Simmonsia.

Evolution and taxonomic split of the model grass Brachypodium distachyon

BACKGROUND AND AIMS

Brachypodium distachyon is being widely investigated across the world as a model plant for temperate cereals. This annual plant has three cytotypes (2n = 10, 20, 30) that are still regarded as part of a single species. Here, a multidisciplinary study has been conducted on a representative sampling of the three cytotypes to investigate their evolutionary relationships and origins, and to elucidate if they represent separate species.

METHODS

Statistical analyses of 15 selected phenotypic traits were conducted in individuals from 36 lines or populations. Cytogenetic analyses were performed through flow cytometry, fluorescence in situ hybridization (FISH) with genomic (GISH) and multiple DNA sequences as probes, and comparative chromosome painting (CCP). Phylogenetic analyses were based on two plastid (ndhF, trnLF) and five nuclear (ITS, ETS, CAL, DGAT, GI) genes from different Brachypodium lineages, whose divergence times and evolutionary rates were estimated.

KEY RESULTS

The phenotypic analyses detected significant differences between the three cytotypes and demonstrated stability of characters in natural populations. Genome size estimations, GISH, FISH and CCP confirmed that the 2n = 10 and 2n = 20 cytotypes represent two different diploid taxa, whereas the 2n = 30 cytotype represents the allotetraploid derived from them. Phylogenetic analysis demonstrated that the 2n = 20 and 2n = 10 cytotypes emerged from two independent lineages that were, respectively, the maternal and paternal genome donors of the 2n = 30 cytotype. The 2n = 20 lineage was older and mutated significantly faster than the 2n = 10 lineage and all the core perennial Brachypodium species.

CONCLUSIONS

The substantial phenotypic, cytogenetic and molecular differences detected among the three B. distachyon sensu lato cytotypes are indicative of major speciation processes within this complex that allow their taxonomic separation into three distinct species. We have kept the name B. distachyon for the 2n = 10 cytotype and have described two novel species as B. stacei and B. hybridum for, respectively, the 2n = 20 and 2n = 30 cytotypes.

An updated nomenclature for keratin-associated proteins (KAPs)

Most protein in hair and wool is of two broad types: keratin intermediate filament-forming proteins (commonly known as keratins) and keratin-associated proteins (KAPs). Keratin nomenclature was reviewed in 2006, but the KAP nomenclature has not been revised since 1993. Recently there has been an increase in the number of KAP genes (KRTAPs) identified in humans and other species, and increasingly reports of variation in these genes. We therefore propose that an updated naming system is needed to accommodate the complexity of the KAPs. It is proposed that the system is founded in the previous nomenclature, but with the abbreviation sp-KAPm-nL*x for KAP proteins and sp-KRTAPm-n(p/L)*x for KAP genes. In this system “sp” is a unique letter-based code for different species as described by the protein knowledge-based UniProt. “m” is a number identifying the gene or protein family, “n” is a constituent member of that family, “p” signifies a pseudogene if present, “L” if present signifies “like” and refers to a temporary “place-holder” until the family is confirmed and “x” signifies a genetic variant or allele. We support the use of non-italicised text for the proteins and italicised text for the genes.

This nomenclature is not that different to the existing system, but it includes species information and also describes genetic variation if identified, and hence is more informative. For example, GenBank sequence JN091630 would historically have been named KRTAP7-1 for the gene and KAP7-1 for the protein, but with the proposed nomenclature would be SHEEP-KRTAP7-1*A and SHEEP-KAP7-1*A for the gene and protein respectively. This nomenclature will facilitate more efficient storage and retrieval of data and define a common language for the KAP proteins and genes from all mammalian species.

Pterospoda nigrescens (Hulst), a synonym of Ixala klotsi Sperry (Lepidoptera, Geometridae, Ennominae)

Comparison of the types of Ixala klotsi (Sperry) and Pterospoda nigrescens (Hulst) shows that they are the same species, with Ixala klotsi a synonym of Pterospoda nigrescens. A lectotype of Selidosema nigrescens is designated, and the types of Selidosema nigrescens and Ixala klotsi are illustrated. Male and female habitus and genitalia of Pterospoda nigrescens are illustrated.

Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family

BACKGROUND

The SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain is an evolutionarily conserved sequence of approximately 130-150 amino acids, and constitutes the catalytic site of lysine methyltransferases (KMTs). KMTs perform many crucial biological functions via histone methylation of chromatin. Histone methylation marks are interpreted differently depending on the histone type (i.e. H3 or H4), the lysine position (e.g. H3K4, H3K9, H3K27, H3K36 or H4K20) and the number of added methyl groups (i.e. me1, me2 or me3). For example, H3K4me3 and H3K36me3 are associated with transcriptional activation, but H3K9me2 and H3K27me3 are associated with gene silencing. The substrate specificity and activity of KMTs are determined by sequences within the SET domain and other regions of the protein.

RESULTS

Here we identified 49 SET-domain proteins from the recently sequenced Brassica rapa genome. We performed sequence similarity and protein domain organization analysis of these proteins, along with the SET-domain proteins from the dicot Arabidopsis thaliana, the monocots Oryza sativa and Brachypodium distachyon, and the green alga Ostreococcus tauri. We showed that plant SET-domain proteins can be grouped into 6 distinct classes, namely KMT1, KMT2, KMT3, KMT6, KMT7 and S-ET. Apart from the S-ET class, which has an interrupted SET domain and may be involved in methylation of nonhistone proteins, the other classes have characteristics of histone methyltransferases exhibiting different substrate specificities: KMT1 for H3K9, KMT2 for H3K4, KMT3 for H3K36, KMT6 for H3K27 and KMT7 also for H3K4. We also propose a coherent and rational nomenclature for plant SET-domain proteins. Comparisons of sequence similarity and synteny of B. rapa and A. thaliana SET-domain proteins revealed recent gene duplication events for some KMTs.

CONCLUSION

This study provides the first characterization of the SET-domain KMT proteins of B. rapa. Phylogenetic analysis data allowed the development of a coherent and rational nomenclature of this important family of proteins in plants, as in animals. The results obtained in this study will provide a base for nomenclature of KMTs in other plant species and facilitate the functional characterization of these important epigenetic regulatory genes in Brassica crops.

A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names

A personal synopsis of the decisions made at the Nomenclature Section meeting of the International Botanical Congress in Melbourne in July 2011 is provided, with an emphasis on those which will affect the working practices of, or will otherwise be of interest to, mycologists. The topics covered include the re-naming of the Code, the acceptance of English as an alternative to Latin for validating diagnoses, conditions for permitting electronic publication of names, mandatory deposit of key nomenclatural information in a recognized repository for the valid publication of fungal names, the discontinuance of dual nomenclature for pleomorphic fungi, clarification of the typification of sanctioned names, and acceptability of names originally published under the zoological code. Collectively, these changes are the most fundamental to have been enacted at a single Congress since the 1950s, and herald the dawn of a new era in the practice of fungal nomenclature.

Resurrection of the genus Staphisagria J. Hill, sister to all the other Delphinieae (Ranunculaceae)

Molecular sequence data show that the three species oDelphinium subg. Staphisagria (J. Hill) Peterm. form the sister clade to Aconitum L., Aconitella SpachConsolida (DC.) S.F. Gray, and all remaining species of Delphinium L. To account for this finding we resurrect Staphisagria J. Hill (1756). Names in Staphisagria are available for two of the species. We here make the required new combination for the third species, Staphisagria picta (Willd.) F. Jabbour, provide a key to the species, and illustrate one of them.

Family-group names for termites (Isoptera), redux

Forty-eight family-group names are identified for insects among the Isoptera (termites), representing a nearly 19% increase since the last compilation less than 10 years ago. Accordingly, these names are newly catalogued, including various updates from the original summary. The name Reticulitermitidae is recognized as a nomen nudum while Caatingatermitinae is newly considered a nomen invalidum, and neither is available in zoological nomenclature. A catalogue of the suprafamilial names for Isoptera is appended. The name Xylophagodea is formally proposed for the Isoptera + Cryptocercidae clade.

A revision of Cyanonectria and Geejayessia gen. nov., and related species with Fusarium-like anamorphs

A revision of Fusarium-like species associated with the plant genus Buxus led to a reconsideration of generic concepts in the Fusarium clade of the Nectriaceae. Phylogenetic analyses of the partial second largest subunit of the RNA polymerase II (rpb2) and the larger subunit of the ATP citrate lyase (acl1) gene exons confirm the existence of a clade, here called the terminal Fusarium clade, that includes genera such as Fusariumsensu stricto (including its Gibberella teleomorphs), Albonectria, Cyanonectria, “Haematonectria”, the newly described genus Geejayessia, and “Nectria” albida. Geejayessia accommodates five species. Four were previously classified in Nectria sensu lato, namely the black perithecial, KOH–species G. atrofusca and the orange or reddish, KOH+ G. cicatricum, G. desmazieri and G. zealandica.Geejayessia celtidicola is newly described. Following our phylogenetic analyses showing its close relationship with Cyanonectria cyanostoma, the former Gibbera buxi is recombined as the second species of Cyanonectria. A three gene phylogenetic analysis of multiple strains of each morphological species using translation elongation factor 1 α (tef-1), rpb2 and acl1 gene exons and introns confirms their status as distinct phylogenetic species. Internal transcribed spacer of the ribosomal RNA gene cluster and nuclear large ribosomal subunit sequences were generated as additional DNA barcodes for selected strains. The connection of Fusarium buxicola, often erroneously reported as the anamorph of G. desmazieri, with the bluish black and KOH+ perithecial species C. buxi is reinstated. Most Cyanonectria and Geejayessia species exhibit restricted host ranges on branches or twigs of Buxus species, Celtisoccidentalis, or Staphyleatrifolia. Their perithecia form caespitose clusters on well-developed, mostly erumpent stromata on the bark or outer cortex of the host and are relatively thin-walled, mostly smooth, and therefore reminiscent of the more or less astromatous, singly occurring perithecia of Cosmospora, Dialonectria, and Microcera. The cell walls in outer- and inner layers of the perithecial walls of Cyanonectria and Geejayessia have inconspicuous pore-like structures, as do representative species of Albonectria, Fusarium sensu stricto, “Haematonectria”, and “Nectria” albida. The taxonomic significance of these structures, which we call Samuels' pores, is discussed.

Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium

Over 200 new sequences are generated for members of the genus Acremonium and related taxa including ribosomal small subunit sequences (SSU) for phylogenetic analysis and large subunit (LSU) sequences for phylogeny and DNA-based identification. Phylogenetic analysis reveals that within the Hypocreales, there are two major clusters containing multiple Acremonium species. One clade contains Acremonium sclerotigenum, the genus Emericellopsis, and the genus Geosmithia as prominent elements. The second clade contains the genera Gliomastixsensu stricto and Bionectria. In addition, there are numerous smaller clades plus two multi-species clades, one containing Acremonium strictum and the type species of the genus Sarocladium, and, as seen in the combined SSU/LSU analysis, one associated subclade containing Acremonium breve and related species plus Acremonium curvulum and related species. This sequence information allows the revision of three genera. Gliomastix is revived for five species, G. murorum, G. polychroma, G. tumulicola, G. roseogrisea, and G. masseei. Sarocladium is extended to include all members of the phylogenetically distinct A. strictum clade including the medically important A. kiliense and the protective maize endophyte A. zeae. Also included in Sarocladium are members of the phylogenetically delimited Acremonium bacillisporum clade, closely linked to the A. strictum clade. The genus Trichothecium is revised following the principles of unitary nomenclature based on the oldest valid anamorph or teleomorph name, and new combinations are made in Trichothecium for the tightly interrelated Acremonium crotocinigenum, Spicellum roseum, and teleomorph Leucosphaerinaindica. Outside the Hypocreales, numerous Acremonium-like species fall into the Plectosphaerellaceae, and A. atrogriseum falls into the Cephalothecaceae.

One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR

Some fungi with pleomorphic life-cycles still bear two names despite more than 20 years of molecular phylogenetics that have shown how to merge the two systems of classification, the asexual "Deuteromycota" and the sexual "Eumycota". Mycologists have begun to flout nomenclatorial regulations and use just one name for one fungus. The International Code of Botanical Nomenclature (ICBN) must change to accommodate current practice or become irrelevant. The fundamental difference in the size of fungi and plants had a role in the origin of dual nomenclature and continues to hinder the development of an ICBN that fully accommodates microscopic fungi. A nomenclatorial crisis also looms due to environmental sequencing, which suggests that most fungi will have to be named without a physical specimen. Mycology may need to break from the ICBN and create a MycoCode to account for fungi known only from environmental nucleic acid sequence (i.e. ENAS fungi).

Family-group names in Coleoptera (Insecta)

We synthesize data on all known extant and fossil Coleoptera family-group names for the first time. A catalogue of 4887 family-group names (124 fossil, 4763 extant) based on 4707 distinct genera in Coleoptera is given. A total of 4492 names are available, 183 of which are permanently invalid because they are based on a preoccupied or a suppressed type genus. Names are listed in a classification framework. We recognize as valid 24 superfamilies, 211 families, 541 subfamilies, 1663 tribes and 740 subtribes. For each name, the original spelling, author, year of publication, page number, correct stem and type genus are included. The original spelling and availability of each name were checked from primary literature. A list of necessary changes due to Priority and Homonymy problems, and actions taken, is given. Current usage of names was conserved, whenever possible, to promote stability of the classification.New synonymies (family-group names followed by genus-group names): Agronomina Gistel, 1848 syn. nov. of Amarina Zimmermann, 1832 (Carabidae), Hylepnigalioini Gistel, 1856 syn. nov. of Melandryini Leach, 1815 (Melandryidae), Polycystophoridae Gistel, 1856 syn. nov. of Malachiinae Fleming, 1821 (Melyridae), Sclerasteinae Gistel, 1856 syn. nov. of Ptilininae Shuckard, 1839 (Ptinidae), Phloeonomini Ádám, 2001 syn. nov. of Omaliini MacLeay, 1825 (Staphylinidae), Sepedophilini Ádám, 2001 syn. nov. of Tachyporini MacLeay, 1825 (Staphylinidae), Phibalini Gistel, 1856 syn. nov. of Cteniopodini Solier, 1835 (Tenebrionidae); Agronoma Gistel 1848 (type species Carabus familiaris Duftschmid, 1812, designated herein) syn. nov. of Amara Bonelli, 1810 (Carabidae), Hylepnigalio Gistel, 1856 (type species Chrysomela caraboides Linnaeus, 1760, by monotypy) syn. nov. of Melandrya Fabricius, 1801 (Melandryidae), Polycystophorus Gistel, 1856 (type species Cantharis aeneus Linnaeus, 1758, designated herein) syn. nov. of Malachius Fabricius, 1775 (Melyridae), Sclerastes Gistel, 1856 (type species Ptilinus costatus Gyllenhal, 1827, designated herein) syn. nov. of Ptilinus Geoffroy, 1762 (Ptinidae), Paniscus Gistel, 1848 (type species Scarabaeus fasciatus Linnaeus, 1758, designated herein) syn. nov. of Trichius Fabricius, 1775 (Scarabaeidae), Phibalus Gistel, 1856 (type species Chrysomela pubescens Linnaeus, 1758, by monotypy) syn. nov. of Omophlus Dejean, 1834 (Tenebrionidae). The following new replacement name is proposed: Gompeliina Bouchard, 2011 nom. nov. for Olotelina Báguena Corella, 1948 (Aderidae).Reversal of Precedence (Article 23.9) is used to conserve usage of the following names (family-group names followed by genus-group names): Perigonini Horn, 1881 nom. protectum over Trechicini Bates, 1873 nom. oblitum (Carabidae), Anisodactylina Lacordaire, 1854 nom. protectum over Eurytrichina LeConte, 1848 nom. oblitum (Carabidae), Smicronychini Seidlitz, 1891 nom. protectum over Desmorini LeConte, 1876 nom. oblitum (Curculionidae), Bagoinae Thomson, 1859 nom. protectum over Lyprinae Gistel 1848 nom. oblitum (Curculionidae), Aterpina Lacordaire, 1863 nom. protectum over Heliomenina Gistel, 1848 nom. oblitum (Curculionidae), Naupactini Gistel, 1848 nom. protectum over Iphiini Schönherr, 1823 nom. oblitum (Curculionidae), Cleonini Schönherr, 1826 nom. protectum over Geomorini Schönherr, 1823 nom. oblitum (Curculionidae), Magdalidini Pascoe, 1870 nom. protectum over Scardamyctini Gistel, 1848 nom. oblitum (Curculionidae), Agrypninae/-ini Candèze, 1857 nom. protecta over Adelocerinae/-ini Gistel, 1848 nom. oblita and Pangaurinae/-ini Gistel, 1856 nom. oblita (Elateridae), Prosternini Gistel, 1856 nom. protectum over Diacanthini Gistel, 1848 nom. oblitum (Elateridae), Calopodinae Costa, 1852 nom. protectum over Sparedrinae Gistel, 1848 nom. oblitum (Oedemeridae), Adesmiini Lacordaire, 1859 nom. protectum over Macropodini Agassiz, 1846 nom. oblitum (Tenebrionidae), Bolitophagini Kirby, 1837 nom. protectum over Eledonini Billberg, 1820 nom. oblitum (Tenebrionidae), Throscidae Laporte, 1840 nom. protectum over Stereolidae Rafinesque, 1815 nom. oblitum (Throscidae) and Lophocaterini Crowson, 1964 over Lycoptini Casey, 1890 nom. oblitum (Trogossitidae); Monotoma Herbst, 1799 nom. protectum over Monotoma Panzer, 1792 nom. oblitum (Monotomidae); Pediacus Shuckard, 1839 nom. protectum over Biophloeus Dejean, 1835 nom. oblitum (Cucujidae), Pachypus Dejean, 1821 nom. protectum over Pachypus Billberg, 1820 nom. oblitum (Scarabaeidae), Sparrmannia Laporte, 1840 nom. protectum over Leocaeta Dejean, 1833 nom. oblitum and Cephalotrichia Hope, 1837 nom. oblitum (Scarabaeidae).

Outcomes of the 2011 Botanical Nomenclature Section at the XVIII International Botanical Congress

The Nomenclature Section held just before the 18th International Botanical Congress in Melbourne, Australia in July 2011 saw sweeping changes to the way scientists name new plants, algae, and fungi. The changes begin on the cover: the title was broadened to make explicit that the Code applies not only to plants, but also to algae and fungi. The new title will now be the International Code of Nomenclature of algae, fungi, and plants. For the first time in history the Code will allow for the electronic publication of names of new taxa. In an effort to make the publication of new names more accurate and efficient, the requirement for a Latin validating diagnosis or description was changed to allow either English or Latin for these essential components of the publication of a new name. Both of these latter changes will take effect on 1 January 2012. The nomenclatural rules for fungi will see several important changes, the most important of which is probably the adoption of the principle of "one fungus, one name." Paleobotanists will also see changes with the elimination of the concept of "morphotaxa" from the Code.

Lectotypifications, synonymy, and a new name in Capsicum (Solanoideae, Solanaceae)

Considerable confusion exists within Capsicum (Solanaceae) regarding the status and typification of several names, in part due to misidentifications. Some types were destroyed in Berlin during the Second World War, some have not been found by modern systematics, while others exhibit uncertain locality data or contain material from more than one species. Fourteen lectotypes, synonyms, and a new name, Capsicum eshbaughii Barboza nom. nov.,are proposed here.

Mixed incontinence: comparing definitions in non-surgical patients

PURPOSE

We aimed to explore operational definitions of mixed urinary incontinence (MUI) for use in incontinence outcomes research for non-surgical patient populations.

METHODS

A secondary analysis of women with urge incontinence or urge predominant MUI enrolled in the Urinary Incontinence Treatment Network BE-DRI randomized clinical trial was performed. Subjects were characterized at baseline for urinary incontinence severity and incontinence subtype (stress or urge) using the Medical, Epidemiologic, and Social Aspects of Aging (MESA) questionnaire, the Urogenital Distress Inventory, and a 7-day urinary diary. Various different definitions of MUI, ranging from low to high threshold, were created using a combination of these baseline incontinence measures. Prevalence of MUI based on each definition was described and compared to treatment response. Logistic regression analysis was used to estimate the association between the study outcomes and the different definitions of MUI.

RESULTS

The 307 participants in the BE-DRI study had a mean age of 56.9 (± 13.9) years with a mean total MESA score of 21.7 (± 8.9) and a mean total UDI score of 120.5 (± 49.6). The proportion of women diagnosed with MUI varied significantly by definition ranging from 63.5% to 96.4%. Low threshold symptom-based definitions resulted in nearly universal diagnosis of MUI. No strict cut-off value for these baseline measures was identified to predict clinical outcomes.

CONCLUSIONS

Current MUI definitions do not adequately categorize clinically relevant UI subgroups. For research purposes we believe it necessary to describe the severity of each incontinence subtype separately in subjects with MUI.

A revision of the genus Antepione Packard with description of the new genus Pionenta Ferris (Lepidoptera, Geometridae, Ennominae)

Based on genitalic studies, the new genus Pionenta is established for two taxa formerly placed under Antepione. The taxa hewesata and ochreata (and previously associated synonyms) are now synonomized as Pionenta ochreata. Three species of Antepione are now recognized: Antepione thisoaria, Antepione imitata, Antepione tiselaaria with the taxa comstocki, constans, and indiscretata synonomized under Antepione imitata. No new species are described. Adults and genitalia are illustrated, including type specimens.

Molecular rDNA phylogeny of Telotylenchidae Siddiqi, 1960 and evaluation of tail termini

Three stunt nematode species, Tylenchorhynchus leviterminalis, T. dubius and T. claytoni were characterized with segments of small subunit 18S and large subunit 28S rDNA sequence and placed in molecular phylogenetic context with other polyphyletic taxa of Telotylenchidae. Based upon comparably sized phylogenetic breadth of outgroups and ingroups, the 28S rDNA contained three times the number of phylogenetically informative alignment characters relative to the alignment total compared to the larger 18S dataset even though there were fewer than half the number of taxa represented. Tail shapes and hyaline termini were characterized for taxa within these subfamily trees, and variability discussed for some related species. In 18S trees, similar terminal tail thickness was found in a well-supported clade of three Tylenchorhynchus: broad-tailed T. leviterminalis branched outside relatively narrow-tailed T. claytoni and T. nudus. Terminal tail thickness within Merliniinae, Telotylenchinae and related taxa showed a mosaic distribution. Thick-tailed Trophurus, Macrotrophurus and putative Paratrophurus did not group together in the 18S tree. Extremely thickened tail termini arose at least once in Amplimerlinius and Pratylenchoides among ten species of Merliniinae plus three Pratylenchoides, and three times within twelve taxa of Telotylenchinae and Trophurinae. Conflicting generic and family nomenclature based on characters such as pharyngeal overlap are discussed in light of current molecular phylogeny. Contrary to some expectations from current taxonomy, Telotylenchus and Tylenchorhynchus cf. robustus did not cluster with three Tylenchorhynchus spp. Two putative species of Neodolichorhynchus failed to group together, and two populations of Scutylenchus quadrifer demonstrated as much or greater genetic distance between them than among three related species of Merlinius.

Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys

We describe a method to publish nomenclatural acts described in taxonomic websites (Scratchpads) that are formally registered through publication in a printed journal (ZooKeys). This method is fully compliant with the zoological nomenclatural code. Our approach supports manuscript creation (via a Scratchpad), electronic act registration (via ZooBank), online and print publication (in the journal ZooKeys) and simultaneous dissemination (ZooKeys and Scratchpads) for nomenclatorial acts including new species descriptions. The workflow supports the generation of manuscripts directly from a database and is illustrated by two sample papers published in the present issue.

Marasmioid and gymnopoid fungi of the Republic of Korea. 2. Marasmius sect. Globulares

Seven species of Marasmius sect. Globulares with smooth pileipellis cells (sect. Globulares s. Singer) have been collected in the Republic of Korea (South Korea) to date, viz. M. aurantioferrugineus, M. brunneospermus, M. maximus, M. nivicola, M. purpureostriatus, M. wynneae and M. fusicystidiosus. Descriptions of their macro- and microscopic features with a discussion of similar taxa are given. Their taxonomic position was confirmed using DNA data. Marasmius fusicystidiosus is described as a new species. A key to aid in their identification is also provided.