Notes on Echinodorus (Alismataceae)

Errors by Rataj in lecto- and neotypification of five names inEchinodorus are corrected. These errors include the selection of lectotype specimens that were not cited in the protologue and the designation of neotypes from syntypes. Lectotypes for four of the names are designated here. The other is not typified at this time, as we have as yet been unable to examine the cited collections. In addition, a lectotype is designated for the Linnaean nameAlisma cordifolia, a name for which Rataj did not choose a lectotype. A new species,Echinodorus reticulatus, is described and illustrated. Five new combinations at the subspecies level are proposed, with most of these subspecies having a distribution from Central America to Paraguay and Argentina.     

A revision of European Copidosoma Ratzeburg (Hymenoptera, Chalcidoidea, Encyrtidae): some corrections and a description of Copidosoma tremblayi sp.nov.

Abstract.  One invalid lectotype designation proposed in a recent revision of European species of Copidosoma is validated ( Encyrtus geniculatus Dalman) and four incorrectly cited designations are corrected ( C. peninsulare Mercet, E. filicornis Dalman, E. flagellaris Dalman, E. machaeras Walker). One species, C. tremblayi , is described as new.     

A comparison of experimental designs for selection in breeding trials with nested treatment structure

Plant breeders frequently evaluate large numbers of entries in field trials for selection. Generally, the tested entries are related by pedigree. The simplest case is a nested treatment structure, where entries fall into groups or families such that entries within groups are more closely related than between groups. We found that some plant breeders prefer to plant close relatives next to each other in the field. This contrasts with common experimental designs such as the α-design, where entries are fully randomized. A third design option is to randomize in such a way that entries of the same group are separated as much as possible. The present paper compares these design options by simulation. Another important consideration is the type of model used for analysis. Most of the common experimental designs were optimized assuming that the model used for analysis has fixed treatment effects. With many entries that are related by pedigree, analysis based on a model with random treatment effects becomes a competitive alternative. In simulations, we therefore study the properties of best linear unbiased predictions (BLUP) of genetic effects based on a nested treatment structure under these design options for a range of genetic parameters. It is concluded that BLUP provides efficient estimates of genetic effects and that resolvable incomplete block designs such as the α-design with restricted or unrestricted randomization can be recommended.     

The impact of random frequency-dependent mutations on the average population fitness

ABSTRACT: BACKGROUND: In addition to selection, the process of evolution is accompanied by stochastic effects, such as changing environmental conditions, genetic drift and mutations. Commonly it is believed that without genetic drift, advantageous mutations quickly fixate in a halpoid population due to strong selection and lead to a continuous increase of the average fitness. This conclusion is based on the assumption of constant fitness. However, for frequency dependent fitness, where the fitness of an individual depends on the interactions with other individuals in the population, this does not hold. RESULTS: We propose a mathematical model that allows to understand the consequences of random frequency dependent mutations on the dynamics of an infinite large population. The frequencies of different types change according to the replicator equations and the fitness of a mutant is random and frequency dependent. To capture the interactions of different types, we employ a payoff matrix of variable size and thus are able to accommodate an arbitrary number of mutations. We assume that at most one mutant type arises at a time. The payoff entries to describe the mutant type are random variables obeying a probability distribution which is related to the fitness of the parent type. CONCLUSIONS: We show that a random mutant can decrease the average fitness under frequency dependent selection, based on analytical results for two types, and on simulations for n types. Interestingly, in the case of at most two types the probabilities to increase or decrease the average fitness are independent of the concrete probability density function. Instead, they only depend on the probability that the payoff entries of the mutant are larger than the payoff entries of the parent type.     

O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins.

O-GLYCBASE is an updated database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the SWISS-PROT database. Entries include information about species, sequence, glycosylation sites and glycan type. O-GLYCBASE is now fully cross-referenced to the SWISS-PROT, PIR, PROSITE, PDB, EMBL, HSSP, LISTA and MIM databases. Compared with version 1.0 the number of entries have increased by 34%. Revision of the O-glycan assignment was performed on 20% of the entries. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through WWW or by anonymous FTP.     

ProtBuD: a database of biological unit structures of protein families and superfamilies

MOTIVATION: Modeling of protein interactions is often possible from known structures of related complexes. It is often time-consuming to find the most appropriate template. Hypothesized biological units (BUs) often differ from the asymmetric units and it is usually preferable to model from the BUs. RESULTS: ProtBuD is a database of BUs for all structures in the Protein Data Bank (PDB). We use both the PDBs BUs and those from the Protein Quaternary Server. ProtBuD is searchable by PDB entry, the Structural Classification of Proteins (SCOP) designation or pairs of SCOP designations. The database provides the asymmetric and BU contents of related proteins in the PDB as identified in SCOP and Position-Specific Iterated BLAST (PSI-BLAST). The asymmetric unit is different from PDB and/or Protein Quaternary Server (PQS) BUs for 52% of X-ray structures, and the PDB and PQS BUs disagree on 18% of entries. AVAILABILITY: The database is provided as a standalone program and a web server from http://dunbrack.fccc.edu/ProtBuD.php.     

Deployment to plantations of numbers and proportions of clones with special emphasis on maximizing gain at a constant diversity

Summary The value of a mixture of genetic entries present in different proportions is defined. A measure of the disadvantage of reduced diversity is defined as the sum of the squares of the proportions of the different entries. An algorithm for maximizing genetic gain of the mixture under the constraint of a constant disadvantage is developed. The optimal deployment strategy is one that lets the proportion of the genetic entries be linearly dependent on their genetic value. By use of rankits as entries for genetic values, optimal solutions for deployment were calculated for a range of values of available entries (from 10 to 5,000) and preset diversity-related disadvantage-factors (the preset values correspond to mixtures of between 2 and 100 entries in identical proportions). The values are tabulated so they can be used by breeders. The superiority of the proposed strategy increases with the proportion of the available entries which are selected. In the situation that around half would have been selected if truncation selection was applied, the improvement in genetic gain compared to classical truncation selection is up to 18%. Thus, considerable improvements in gain are possible without any sacrifice in diversity. Applications are discussed with particular reference to clonal forestry.     

Toward Computational Cumulative Biology by Combining Models of Biological Datasets

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher''s experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations—for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.     

Confusions in orbivirus protein classification

ABSTRACT: An extensive comparative analysis of orbivirus genomes revealed four cases of unclear numeration and protein designation, due to confused reference to protein size or segment size by which they are encoded. A concise nomenclature based on type species, sequence homology and functional characteristics independent of segment or protein size is suggested.     

中国11个双子叶植物原白中排印错误之更正

对我国11个双子叶植物（Dicotyledon）原白中模式标本引证的排印错误做了更正：砚山锥栗（壳斗科）原白中错误地将模式标本引证为王启无84116,实际应为王启无84416,前者属于菊科植物Inuna helianthus-aquatica C.Y.Wu ex Ling。长果柯（壳斗科）原白中错误地将模式标本引证为K.M.Feng 13012,实际应为K.M.Feng 13102,前者属于冬青科植物Ilex triflora Bl.。福建红小麻（荨麻科）原白中错误地将主模式标本引证为C.J.Chen&Z.Y.Li 109,实际应为C.J.Chen&Z.Y.Li 103,前者属于荨麻科植物Oreocnide frutescens（Thunb.）Miq.。少毛全缘叶紫麻（荨麻科）原白中错误地将主模式标本引证为N.K.Chun 44099,实际应为N.K.Chun 44033,前者属于杜鹃花科植物Lyonia ovalifolia（Wallich）Drude var.rubrovenia（Merr.）Judd.。甘南铁线莲（毛茛科）原白中错误地将主模式标本引证为Baishuijiang Exped.4490,实际应为Baishuijiang Exped.4990,前者属于卫矛科植物Euonymus alatus（Thunb.）Sieb.。矮粗距翠雀花（毛茛科）原白中错误地将模式标本引证为Sichuan Veg.Exped.3137,实际应为Sichuan Veg.Exped.3173,前者属于龙胆科植物Gentiana conduplicata T.N.Ho。镇康黄芪（豆科）原白中错误地将主模式标本引证为T.T.Yu 17255,实际应为T.T.Yu 17225,前者属于莎草科植物Scirpus lushanensis Ohwi。宽翼棘豆（豆科）原白中错误地将模式标本引证为Qinghai-Xizang Comp.Exped.9484,实际应为Qinghai-Xizang Comp.Exped.9485,前者属于石竹科植物Arenaria kansuensis Maxim.。肾瓣黄芪（豆科）原白中错误地将模式标本引证为Qinghai-Xizang Comp.Exped.3650,实际应为Qinghai-Xizang Comp.Exped.3605,前者属于麻黄科植物Ephedra gerardiana Wall.ex Mey.。湖南长柄槭（槭树科）原白中错误地将模式标本引证为李泽棠2944,实际应为李泽棠2994,前者属于杜鹃花科植物Pieris formosa D.Don。峨眉勾儿茶（鼠李科）原白中错误地将模式标本引证为杨光辉54729,实际应为杨光辉54723,前者属于山茱萸科植物Helwingia chinensis Batalin.。     

Singing from the Grave: DNA from a 180 Year Old Type Specimen Confirms the Identity of Chrysoperla carnea (Stephens)

Historically serving as repositories for morphologically-based taxonomic research, natural history collections are now increasingly being targeted in studies utilizing DNA data. The development of advanced molecular techniques has facilitated extraction of useable DNA from old specimens, including type material. Sequencing diagnostic molecular markers from type material enables accurate species designation, especially where modern taxonomic hypotheses confirm morphologically cryptic species complexes. One such example is Chrysoperla carnea (Stephens), which belongs to a complex of about 20 cryptic species, most of which can only be reliably distinguished by their pre-mating courtship songs or by DNA analysis. The subtle morphological variation in the group has led to disagreement over the previous designation of the lectotype for C. carnea, an issue that has been further compounded because Chrysoperla carnea is a highly valued biological control agent in arable crops. Archival DNA extraction and sequencing from the 180 year old lectotype specimen, combined with Bayesian and Likelihood based phylogenetic analyses of modern specimens from the entire complex, were used to establish unambiguously the true identity of Chrysoperla carnea.     

The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains

The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project that has been conceived to provide a useful tool especially for the scientific microbial taxonomist community. The aim of what we have called "The All-Species Living Tree" is to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. This tree is to be regularly updated by adding the species with validly published names that appear monthly in the Validation and Notification lists of the International Journal of Systematic and Evolutionary Microbiology. For this purpose, the SAM executive editors, together with the responsible teams of the ARB, SILVA, and LPSN projects (www.arb-home.de, www.arb-silva.de, and www.bacterio.cict.fr, respectively), have prepared a 16S rRNA database containing over 6700 sequences, each of which represents a single type strain of a classified species up to 31 December 2007. The selection of sequences had to be undertaken manually due to a high error rate in the names and information fields provided for the publicly deposited entries. In addition, from among the often occurring multiple entries for a single type strain, the best-quality sequence was selected for the project. The living tree database that SAM now provides contains corrected entries and the best-quality sequences with a manually checked alignment. The tree reconstruction has been performed by using the maximum likelihood algorithm RAxML. The tree provided in the first release is a result of the calculation of a single dataset containing 9975 single entries, 6728 corresponding to type strain gene sequences, as well as 3247 additional high-fquality sequences to give robustness to the reconstruction. Trees are dynamic structures that change on the basis of the quality and availability of the data used for their calculation. Therefore, the addition of new type strain sequences in further subsequent releases may help to resolve certain branching orders that appear ambiguous in this first release. On the web sites: www.elsevier.de/syapm and www.arb-silva.de/living-tree, the All-Species Living Tree team will release a regularly updated database compatible with the ARB software environment containing the whole 16S rRNA dataset used to reconstruct "The All-Species Living Tree". As a result, the latest reconstructed phylogeny will be provided. In addition to the ARB file, a readable multi-FASTA universal sequence editor file with the complete alignment will be provided for those not using ARB. There is also a complete set of supplementary tables and figures illustrating the selection procedure and its outcome. It is expected that the All-Species Living Tree will help to improve future classification efforts by simplifying the selection of the correct type strain sequences. For queries, information updates, remarks on the dataset or tree reconstructions shown, a contact email address has been created (living-tree@arb-silva.de). This provides an entry point for anyone from the scientific community to provide additional input for the construction and improvement of the first tree compiling all sequenced type strains of all prokaryotic species for which names had been validly published.     

Experience of an interactive program in undergraduate investigative practicals

A microcomputer program is described which has been used by first-year undergraduates throughout an investigation in microbiology, totalling five hours of practical work. The computer is used by students to check their suggestions of possible lines of investigation, the results of practical procedures, and the decisions made on the basis of this experimental evidence. The program offers advice when entries which are inadvisable or incorrect are entered thus providing guidance without usurping student control of the investigation. Evidence for the effectiveness of this program is presented and the potential for this type of consultative program in other areas is indicated. Based on this experience, advice is offered on the general design of this type of program.     

Revision of the Fabriciinae genus Fabriciola Friedrich, 1939 (Polychaeta: Sabellidae)

The Sabellidae polychaete genus Fabriciola Friedrich is revised as a result of examination of as much of the type material as possible. The type species for the genus has been confused. The earliest designation appears to be Fabricia (Manayunkia) spongicola Southern, 1921, by Ushakov [ Akad. Nauk. SSSR, Opredeliteli po Faune SSSR 56: 1–445 (1955)], whereas subsequent works have incorrectly referred to Manayunkia pacifica Annenkova, 1934, as the type species. The following species are redescribed: Fabriciola baltica Friedrich, 1939, F. berkeleyi Banse, 1956, F. ghardaqa Banse, 1959 a . A new species, F. mediaseta, is described. A neotype is designated for F . baltica. Existence of the type material of F. spongicola (Southern), F. pacifica (Annenkova), and F. tonerella Banse, 1959 b is unknown, but these species are discussed in relation to species examined.     

Typification of Smittium, an important genus in the taxonomy of Harpellales

The Harpellales genus Smittium is based on a type species, S. arvernense, which was described by Poisson in 1937 without designation of a type specimen. Smittium arvernense has not been reported since its original publication. Because the other 79 species of Smittium cannot be compared to the type species, a lectotype is proposed as well as an epitype for that lectotype that is also the holotype of S. mucronatum. Because Smittium is believed to be polyphyletic these type designations will provide stable application of names and, as well resolved phylogenetic analyses of member species emerge based on morphological and DNA sequence characters, they will provide a foundation for a more robust and revised classification.     

LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces.

We continued our effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. As in previous editions the genetic names are consistently associated to each sequence with a known and confirmed ORF. If necessary, synonyms are given in the case of allelic duplicated sequences. Although the first publication of a sequence gives-according to our rules-the genetic name of a gene, in some instances more commonly used names are given to avoid nomenclature problems and the use of ancient designations which are no longer used. In these cases the old designation is given as synonym. Thus sequences can be found either by the name or by synonyms given in LISTA. Each entry contains the genetic name, the mnemonic from the EMBL data bank, the codon bias, reference of the publication of the sequence, Chromosomal location as far as known, SWISSPROT and EMBL accession numbers. New entries will also contain the name from the systematic sequencing efforts. Since the release of LISTA4.1 we update the database continuously. To obtain more information on the included sequences, each entry has been screened against non-redundant nucleotide and protein data bank collections resulting in LISTA-HON and LISTA-HOP. This release includes reports from full Smith and Watermann peptide-level searches against a non-redundant protein sequence database. The LISTA data base can be linked to the associated data sets or to nucleotide and protein banks by the Sequence Retrieval System (SRS). The database is available by FTP and on World Wide Web.     

Comparison of partial tuf gene sequences for the identification of lactobacilli

Comparative analysis of partial tuf sequences was evaluated for the identification and differentiation of lactobacilli. Comparison of the amino acid sequences allowed differentiation between species and also between the subspecies of Lactobacillus delbrueckii. The nucleotide sequence comparison allowed differentiation between other subspecies and between some strains. Lactobacilli from several collections and isolates from dairy samples were clearly identified by comparison of short tuf sequences with those of the type strains. In evaluating the taxonomy of the Lactobacillus casei-related taxa, different tuf amino acid signatures are in favour of a classification into three distinct species. The type strain designation for the L. casei species is discussed.     

O-GLYCBASE: a revised database of O-glycosylated proteins.

O-GLYCBASE is a comprehensive database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the SWISS-PROT and PIR databases as well as directly from recently published reports. Nineteen percent of the entries extracted from the databases needed revision with respect to O-linked glycosylation. Entries include information about species, sequence, glycosylation site and glycan type, and are fully referenced. Sequence logos displaying the acceptor specificity for the GaINAc transferase are shown. A neural network method for prediction of mucin type O-glycosylation sites in mammalian glycoproteins exclusively from the primary sequence is made available by E-mail or WWW. The O-GLYCBASE database is also available electronically through our WWW server or by anonymous FTP.