A step-by-step classification algorithm of protein secondary structures based on double-layer SVM model

In this paper, a step-by-step classification algorithm based on double-layer SVM model is constructed to predict the secondary structure of proteins. The most important feature of this algorithm is to improve the prediction accuracy of α+β and α/β classes through transforming the prediction of two classes of proteins, α+β and α/β classes, with low accuracy in the past, into the prediction of all-α and all-β classes with high accuracy. A widely-used dataset, 25PDB dataset with sequence similarity lower than 40%, is used to evaluate this method. The results show that this method has good performance, and on the basis of ensuring the accuracy of other three structural classes of proteins, the accuracy of α+β class proteins is improved significantly.     

New species of subgenus Tipula (Sivatipula) from China,with redescription of T. (S.) parvauricula and a key to all known species of the Oriental Region (Diptera,Tipulidae, Tipula)

Species of Tipula (Sivatipula) biprocessa sp. n. from Guangxi, China is described and illustrated as new in the subgenus Tipula (Sivatipula) Alexander, 1964. Tipula (Sivatipula) parvauricula Alexander, 1941 is redescribed and illustrated based on additional morphological characters. Semen pump of this subgenus is discussed. A key to all described species in this group is compiled.     

Revision of the genus Ficiana Ghauri and its relationship to other genera in Empoascini (Hemiptera,Cicadellidae, Typhlocybinae)

The empoascine genus Ficiana Ghauri is reviewed based on specimens from China. One new Ficiana species, Ficiana aurantia sp. n. is described from Guangxi in south China. An identification key to all species in this genus is provided. The morphological characters of Ficiana and related genera in this tribe are discussed.     

A new species of Liolaemus related to L. nigroviridis from the Andean highlands of Central Chile (Iguania,Liolaemidae)

The Liolaemus nigroviridis group is a clade of highland lizards endemic to Chile. These species are distributed from northern to central Chile, and currently there are no cases of sympatric distribution. This study describes a new species, Liolaemus uniformis sp. n., from this group, and provides a detailed morphological characterization and mitochondrial phylogeny using cytochrome-b. Liolaemus uniformis was found in sympatry with Liolaemus nigroviridis but noticeably differed in size, scalation, and markedly in the color pattern, without sexual dichromatism. This new species has probably been confused with Liolaemus monticola and Liolaemus bellii, both of which do not belong to the nigroviridis group. The taxonomic issues of this group that remain uncertain are also discussed.     

Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B. anthracis from the B. cereus group

Bacillus anthracis, the causative agent of anthrax, is a potential source of bioterrorism. The existing assays for its identification lack specificity due to the close genetic relationship it exhibits to other members of the B. cereus group. Our comparative analyses of protein sequences from Bacillus species have identified a 24 amino acid deletion in a conserved region of the YeaC protein that is uniquely present in B. anthracis. PCR primers based on conserved regions flanking this indel in the Bacillus cereus group of species (viz. Bacillus cereus, B. anthracis, B. thuringiensis, B. mycoides, B. weihenstephnensis and B. pseudomycoides) specifically amplified a 282 bp fragment from all six reference B. anthracis strains, whereas a 354 bp fragment was amplified from 15 other B. cereus group of species/strains. These fragments, due to large size difference, are readily distinguished by means of agarose gel electrophoresis. In contrast to the B. cereus group, no PCR amplification was observed with any of the non-B. cereus group of species/strains. This indel was also used for developing a rapid pyrosequencing assay for the identification of B. anthracis. Its performance was evaluated by examining the presence or absence of this indel in a panel of 81 B. cereus-like isolates from various sources that included 39 B. anthracis strains. Based upon the sequence data from the pyrograms, the yeaC indel was found to be a distinctive characteristic of various B. anthracis strains tested and not found in any other species/strains from these samples. Therefore, this B. anthracis specific indel provides a robust and highly-specific chromosomal marker for the identification of this high-risk pathogen from other members of the B. cereus group independent of a strain's virulence. The pyrosequencing platform also allows for the rapid and simultaneous screening of multiple samples for the presence of this B. anthracis-specific marker.     

Salinomyces polonicus: A moderately halophilic kin of the most extremely halotolerant fungus Hortaea werneckii

A clade where the most halotolerant fungus in the world – Hortaea werneckii, belongs (hereafter referred to as Hortaea werneckii lineage) includes five species: Hortaea werneckii, H. thailandica, Stenella araguata, Eupenidiella venezuelensis, and Magnuscella marina, of which the first species attracts increasing attention of mycologists. The species diversity and phylogenetic relationships within this lineage are weakly known. In this study two moderately halophilic black yeast strains were isolated from brine of graduation tower in Poland. Molecular phylogenetic analyses based on the rDNA ITS1-5.8S-ITS2 (=ITS), rDNA 28S D1–D2 (=LSU), and RNA polymerase II (rpb2) sequences showed that the two strains belong to Hortaea werneckii lineage but cannot be assigned to any described taxa. Accordingly, a new genus and species, Salinomyces and Salinomyces polonicus, are described for this fungus. Furthermore, molecular phylogenetic analyses have revealed that Hortaea thailandica is more closely related to S. polonicus than to H. werneckii. A new combination Salinomyces thailandicus is proposed for this fungus.     

Publication of descriptions of novel bacterial taxa in <Emphasis Type="Italic">Antonie van Leeuwenhoek</Emphasis>

The species from the order Neisseriales are currently distinguished from other bacteria on the basis of branching in 16S rRNA gene trees. For this order containing a single family, Neisseriaceae, no distinctive molecular, biochemical, or phenotypic characters are presently known. We report here detailed phylogenetic and comparative analyses on the 27 genome sequenced species of the order Neisseriales. Our comparative genomic analyses have identified 54 conserved signature indels (CSIs) in widely distributed proteins that are specific for either all of the sequenced Neisseriales species or a number of clades within this order that are also supported by phylogenetic analyses. Of these CSIs, 11 are specifically present in all of the sequenced species from this order, but are not found in homologous proteins from any other bacteria. These CSIs provide novel molecular markers specific for, and delimiting, this order. Twenty-one CSIs in diverse proteins are specific for a group comprised of the genera Neisseria, Eikenella, Kingella, and Simonsiella (Clade I), which are obligate host-associated organisms, lacking flagella and exhibiting varied morphology. The species from these genera also formed a strongly supported clade in phylogenetic trees based upon concatenated protein sequences; a monophyletic grouping of these genera and other genera displaying similar morphological characteristics was also observed in the 16S rRNA gene tree. A second clade (Clade II), supported by seven of the identified CSIs and phylogenetic trees based upon concatenated protein sequences, grouped together species from the genera Chromobacterium, Laribacter, and Pseudogulbenkiania that are rod-shaped bacteria, which display flagella-based motility and are capable of free living. The remainder of the CSIs were uniquely shared by smaller groups within these two main clades. Our analyses also provide novel insights into the evolutionary history of the Neisseriales and suggest that the CSIs that are specific for the Clade I species may play an important role in the evolution of obligate host-association within this order. On the basis of phylogenetic analysis, the identified CSIs, and conserved phenotypic characteristics of different Neisseriales genera, we propose a division of this order into two families: an emended family Neisseriaceae (corresponding to Clade I) containing the genera Alysiella, Bergeriella, Conchiformibius, Eikenella, Kingella, Neisseria, Simonsiella, Stenoxybacter, Uruburuella and Vitreoscilla and a new family, Chromobacteriaceae fam. nov., harboring the remainder of the genera from this order (viz. Andreprevotia, Aquaspirillum, Aquitalea, Chitinibacter, Chitinilyticum, Chitiniphilus, Chromobacterium, Deefgea, Formivibrio, Gulbenkiania, Iodobacter, Jeongeupia, Laribacter, Leeia, Microvirgula, Paludibacterium, Pseudogulbenkiania, Silvimonas, and Vogesella).     

Phylogeny and phylogeography of the genus Patella based on mitochondrial DNA sequence data

Although some molecular phylogenies of Patella species have been published in recent years, unresolved questions concerning the phylogeny and taxonomy of this genus still remain. We sequenced the mitochondrial genes cytochrome c oxidase subunit I, 12S rRNA and 16S rRNA for all Patella species (Patella vulgata, Patella depressa, Patella candei, Patella caerulea, Patella lugubris, Patella ferruginea, Patella pellucida and the continental and Macaronesian forms of Patella ulyssiponensis and Patella rustica) and Cymbula safiana. Our results revealed the occurrence of five strongly supported clades, although relationships between these are not well supported. According to our data P. vulgata is a genetically distinct lineage and the close phylogenetic relationship between this species and P. depressa, found in previous mitochondrial DNA studies, is not supported. The Mediterranean Sea and the Macaronesian Islands seem to have played an important role in the speciation and diversification of this genus, although different clades show different phylogeographic patterns. Our dataset point to the necessity of a taxonomic revision, as P. candei is paraphyletic relative to P. lugubris.     

The New Caledonian genus Caledonotrichia Sykora (Trichoptera,Insecta) reviewed,with?descriptions?of?6?new species

The New Caledonian endemic hydroptilid genus Caledonotrichia Sykora (Trichoptera) is reviewed and 6 new species are described: Caledonotrichia bifida, Caledonotrichia capensis, Caledonotrichia minuta, Caledonotrichia ouinnica, Caledonotrichia sykorai and Caledonotrichia vexilla. Together with the established species for which revised diagnoses are given, these raise to 11 the number of species known in this genus. The new species, females of 3 species, and several unusual larval cases are examined and described for further insight into relationships of this enigmatic genus. A key to species is provided.     

Two new species of the Liolaemus elongatus-kriegi complex (Iguania,Liolaemidae) from Andean highlands of southern Chile

The elongatus-kriegi complex is one of the most diverse clades of the Liolaemus (sensu stricto) subgenus of lizards. There are currently 29 species recognized in this group distributed between Chile and Argentina. Based on molecular evidence, there seem to be five main clades nested within this complex: the elongatus, leopardinus, kriegi, petrophilus and punmahuida clades. Liolaemus buergeri and Liolaemus kriegi, both of the kriegi clade, were believed to inhabit the surroundings of the Laja Lagoon, in the Biobío Region of Chile. Moreover, this Chilean population of Liolaemus kriegi was recently recognized as an undescribed taxon called “Liolaemus sp. A” based on molecular phylogenetics. In this work, we studied these two populations of the Laja Lagoon and provided the morphological diagnosis to describe them as two new species: Liolaemus scorialis sp. n. and Liolaemus zabalai sp. n., previously considered Liolaemus buergeri and “Liolaemus kriegi/Liolaemus sp. A” respectively. Additionally, we identified another population of Liolaemus scorialis in the vicinity of La Mula Lagoon in the Araucanía Region of Chile. Liolaemus scorialis differs from almost all of the species of the elongatus-kriegi complex by its considerably smaller size. Nevertheless, without molecular data we cannot assign it to any particular subclade. Liolaemus zabalai belongs to the kriegi clade based on published molecular phylogenies. Finally, we provide some natural history data on both species and we document for the first time the presence of Liolaemus neuquensis in Chile from a museum specimen from La Mula Lagoon.     

Monitoring resistance to Bacillus thuringiensis subsp. israelensis in the field by performing bioassays with each Cry toxin separately

Bacillus thuringiensis subsp. israelensis (Bti) is increasingly used worldwide for mosquito control and is the only larvicide used in the French Rhône-Alpes region since decades. The artificial selection of mosquitoes with field-persistent Bti collected in breeding sites from this region led to a moderate level of resistance to Bti, but to relatively high levels of resistance to individual Bti Cry toxins. Based on this observation, we developed a bioassay procedure using each Bti Cry toxin separately to detect cryptic Bti-resistance evolving in field mosquito populations. Although no resistance to Bti was detected in none of the three mosquito species tested (Aedes rusticus, Aedes sticticus and Aedes vexans), an increased tolerance to Cry4Aa (3.5-fold) and Cry11Aa toxins (8-fold) was found in one Ae. sticticus population compared to other populations of the same species, suggesting that resistance to Bti may be arising in this population. This study confirms previous works showing a lack of Bti resistance in field mosquito populations treated for decades with this bioinsecticide. It also provides a first panorama of their susceptibility status to individual Bti Cry toxins. In combination with bioassays with Bti, bioassays with separate Cry toxins allow a more sensitive monitoring of Bti-resistance in the field.     

Morphometric divergence in populations of Anastrepha obliqua (Diptera,Tephritidae) from Colombia and some Neotropical locations

The West Indian fruit fly, Anastrepha obliqua, is one of seven species of quarantine importance of its genus and is one of the most economically important fruit fly pests in Colombia. The taxonomic status of this species is a key issue for further implementation of any pest management program. Several molecular studies have shown enough variability within Anastrepha obliqua to suggest its taxonomic status could be revised; however, there are no morphological studies supporting this hypothesis. The aim of this work was to describe the morphological variability of Colombian populations of Anastrepha obliqua, comparing this variability with that of other samples from the Neotropics. Measurements were performed on individuals from 11 populations collected from different geographic Colombian localities and were compared with populations from Mexico (2), Dominica Island (1), Peru (1) and Brazil (2). Linear morphometric analyses were performed using 23 female morphological traits, including seven variables of the aculeus, three of the thorax, and six of the wing; seven ratios among them were also considered. Discriminant function analyses showed significant morphological differentiation among the Colombian populations, separating them into two groups. Furthermore, in the comparisons between Colombian samples with those from other countries, three clusters were observed. The possibility of finding more than one species within the nominal Anastrepha obliqua population is discussed.     

Detection of Tick-Borne Pathogens in the Korean Water Deer (Hydropotes inermis argyropus) from Jeonbuk Province,Korea

The objective of this study was to investigate the prevalence of tick-borne pathogens in the Korean water deer (Hydropotes inermis argyropus). Pathogens were identified using PCR which included Anaplasma, Ehrlichia, Rickettsia, and Theileria. Rickettsia was not detected, whereas Anaplasma, Ehrlichia, and Theileria infections were detected in 4, 2, and 8 animals, respectively. The most prevalent pathogen was Theileria. Of the 8 Theileria-positive animals, 2 were mixed-infected with 3 pathogens (Anaplasma, Ehrlichia, and Theileria) and another 2 animals showed mixed-infection with 2 pathogens (Anaplasma and Theileria). Sequencing analysis was used to verify the PCR results. The pathogens found in this study were identified as Anaplasma phagocytophilum, Ehrlichia canis, and Theileria sp. To the best of our knowledge, this is the first report identifying these 3 pathogens in the Korean water deer. Our results suggest that the Korean water deer may serve as a major reservoir for these tick-borne pathogens, leading to spread of tick-borne diseases to domestic animals, livestock, and humans. Further studies are needed to investigate their roles in this respect.     

Catabolism of N-Acetylneuraminic Acid,a Fitness Function of the Food-Borne Lactic Acid Bacterium Lactobacillus sakei,Involves Two Newly Characterized Proteins

In silico analysis of the genome sequence of the meat-borne lactic acid bacterium (LAB) Lactobacillus sakei 23K has revealed a repertoire of potential functions related to the adaptation of this bacterium to the meat environment. Among these functions, the ability to use N-acetyl-neuraminic acid (NANA) as a carbon source could provide a competitive advantage for growth on meat in which this amino sugar is present. In this work, we proposed to analyze the functionality of a gene cluster encompassing nanTEAR and nanK (nanTEAR-nanK). We established that this cluster encoded a pathway allowing transport and early steps of the catabolism of NANA in this genome. We also demonstrated that this cluster was absent from the genome of other L. sakei strains that were shown to be unable to grow on NANA. Moreover, L. sakei 23K nanA, nanT, nanK, and nanE genes were able to complement Escherichia coli mutants. Construction of different mutants in L. sakei 23K ΔnanR, ΔnanT, and ΔnanK and the double mutant L. sakei 23K Δ(nanA-nanE) made it possible to show that all were impaired for growth on NANA. In addition, two genes located downstream from nanK, lsa1644 and lsa1645, are involved in the catabolism of sialic acid in L. sakei 23K, as a L. sakei 23K Δlsa1645 mutant was no longer able to grow on NANA. All these results demonstrate that the gene cluster nanTEAR-nanK-lsa1644-lsa1645 is indeed involved in the use of NANA as an energy source by L. sakei.     

Phylogenetic analysis of the sharpshooter genus Subrasaca Young, 1977 (Hemiptera,Cicadellidae, Cicadellini)

The South American sharpshooter genus Subrasaca comprises 14 species. Some species of this genus are quite common in the Brazilian Atlantic Rainforest. In this paper, a phylogenetic analysis of Subrasaca, based on a matrix of 20 terminal taxa and 72 morphological characters of the head, thorax, and male and female genitalia, is presented. The analysis yielded six equally most parsimonious trees (197 steps, CI = 0.6091, RI = 0.5722, and RC = 0.3486). The results suggest that Subrasaca is a monophyletic taxon, although the genus branch is not robust. The clade showing the highest bootstrap and Bremer scores is formed by species with longitudinal dark brown to black stripes on the forewings (Subrasaca bimaculata, Subrasaca constricta, Subrasaca curvovittata, and Subrasaca flavolineata), followed by Subrasaca atronasa + Subrasaca austera.     

Macrolepidoptera biodiversity in Wooster,Ohio from 2001 through 2009

A Skinner mercury vapor light trap was operated from 2001 through 2009 in a residential backyard to document biodiversity within the moth families Thyatiridae, Drepanidae, Geometridae, Mimallonidae, Apatelodidae, Lasiocampidae, Saturniidae, Sphingidae, Erebidae (including Lymantriinae and Arctiinae), Euteliidae, Nolidae, and Noctuidae. When making comparisons to older literature, we recalculated our results to conform to the older classification of the Noctuoidea. Moths were released after identification. There were 501 species documented in 77581 captures from 1290 sampling dates. There was a perceived risk that released moths would fly back into the trap the following evening. This should result in an abnormal number of rare moths that are caught multiple times. The number of species caught twice versus the number caught once was no different than a similar ratio for surveys that used more traditional sampling methods. Therefore this concern does not seem to be valid for these data. These data are provided in a supplementary file available for download.There were three previous surveys conducted in nearby natural areas. They documented fewer species than were documented here. To understand this better, we examined several specialized groups of moths that tend to use host plants not typically found in an urban residential yard. More species in Schinia Hübner, Catocala Schrank, Acronicta Ochsenheimer, and Herminiinae Leech were found in this survey than the other local surveys. Only in the Papaipema Smith did we recover fewer species, though it was still above 70% of what was expected. This diversity could be a result of sampling effort, but it shows that this urban location has a very diverse moth fauna. We suggest that this diversity is partly due to the planting of native plant species in the area about the light trap. Therefore we would concur with others that urban landscapes can be planned to increase biodiversity relevant to more natural ecosystems.In this study we looked at the ratio of the number of species of Geometridae divided by the number of species of Noctuidae as one approach to evaluating the level of disturbance in the moth assemblage. Although the yearly average was nearly constant, the seasonal ratio ranged from 0.09 to 0.91 depending on the sampling date. We also calculated alpha diversity and found that seasonal change in alpha diversity greatly exceeded yearly differences. This strong seasonal component means that a comparison between two studies requires a correction for seasonality and similar sampling intervals. In this study, a shift of two weeks would be sufficient to result in a significant difference in alpha diversity. This is the equivalent of increasing temperature by 1.53 °C. Seasonal shifts limit the usefulness of this methodology for environmental assessment because the within season change exceeds the between season change. This problem is compounded when sampling designs interact with this seasonality.In describing our data, we made use of a growing degree day (GDD) model. This approach corrects for simple temperature dependent shifts in moth biology. Consequently, some of the variability in the data was removed, which should improve the power of statistical tests involving survey data. If sampling protocols were based on growing degree days rather than calendar dates, the bias caused by temperature induced shifts in seasonal cycles could be reduced.     

Root hair formation at the root-hypocotyl junction in CPC-LIKE MYB double and triple mutants of Arabidopsis

In Arabidopsis thaliana, R3-type MYB genes, CAPRICE (CPC) and its family of genes including TRIPTYCHON (TRY), ENHANCER OF TRY AND CPC1 (ETC1), ETC2 and CPC-LIKE MYB3 cooperatively regulate epidermal cell differentiation. Root hair formation is greatly reduced by a mutation in CPC, and try and etc1 enhance this phenotype. In this study, we demonstrate that CPC, TRY and ETC1 are also involved in root hair formation at the root-hypocotyl junction. The cpc try and cpc etc1 double mutants showed a reduced number of root hairs in that area. Additionally, the expression of ETC1::GUS was higher near this area. These results suggest that CPC family of genes also cooperatively regulates root hair formation at the root-hypocotyl junction in unique ways.