Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae)

The rare, monotypic deep-sea fish family Stylephoridae has long been considered a member of the order Lampridiformes (opahs, velifers, ribbonfishes), and no systematic ichthyologist has questioned its placement within the order for over 80 years. Recently three individuals of Stylephorus chordatus were collected from different oceans, and we sequenced the whole mitochondrial genome and a partial nuclear recombination activating gene 1 (RAG1) gene sequences for each specimen. We aligned these sequences with those available from higher teleosts, including representative lampridiforms, and constructed two separate datasets from the sequences. The resulting trees derived from partitioned Bayesian analyses strongly indicated that S. chordatus is not a lampridiform but is closely related to the order Gadiformes (cod and their relatives). Lampridiformes is diagnosed on the basis of four synapomorphies, three of which are correlated with the rare and possibly unique ability to extend both the maxilla and premaxilla as a unit during feeding. Stylephorus also possesses such unique ability, but lacks two and possibly three of the four synapomorphies, suggesting that further morphological analysis is needed. Considering its unique morphologies with no indication of affinities within Gadiformes (or any other presently recognized order), the present results warrant a recognition of the new order for S. chordatus in fish systematics.     

Exploring zipping and assembly as a protein folding principle

It has been proposed that proteins fold by a process called "Zipping and Assembly" (Z&A). Zipping refers to the growth of local substructures within the chain, and assembly refers to the coming together of already-formed pieces. Our interest here is in whether Z&A is a general method that can fold most of sequence space, to global minima, efficiently. Using the HP model, we can address this question by enumerating full conformation and sequence spaces. We find that Z&A reaches the global energy minimum native states, even though it searches only a very small fraction of conformational space, for most sequences in the full sequence space. We find that Z&A, a mechanism-based search, is more efficient in our tests than the replica exchange search method. Folding efficiency is increased for chains having: (a) small loop-closure steps, consistent with observations by Plaxco et al. 1998;277;985-994 that folding rates correlate with contact order, (b) neither too few nor too many nucleation sites per chain, and (c) assembly steps that do not occur too early in the folding process. We find that the efficiency increases with chain length, although our range of chain lengths is limited. We believe these insights may be useful for developing faster protein conformational search algorithms.     

The complete structure of the cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.) chloroplast genome: Its composition and comparative analysis

The complete nucleotide sequence of the cucumber (C. sativus L. var. Borszczagowski) chloroplast genome has been determined. The genome is composed of 155,293 bp containing a pair of inverted repeats of 25,191 bp, which are separated by two single-copy regions, a small 18,222-bp one and a large 86,688-bp one. The chloroplast genome of cucumber contains 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species), with 18 of them located in the inverted repeat region. Of these genes, 16 contain one intron, and two genes and one ycf contain 2 introns. Twenty-one small inversions that form stem-loop structures, ranging from 18 to 49 bp, have been identified. Eight of them show similarity to those of other species, while eight seem to be cucumber specific. Detailed comparisons of ycf2 and ycf15, and the overall structure to other chloroplast genomes were performed.     

Effect of Basic and Acidic Additives on the Separation of Some Basic Drug Enantiomers on Polysaccharide‐Based Chiral Columns With Acetonitrile as Mobile Phase

The separation of enantiomers of 16 basic drugs was studied using polysaccharide‐based chiral selectors and acetonitrile as mobile phase with emphasis on the role of basic and acidic additives on the separation and elution order of enantiomers. Out of the studied chiral selectors, amylose phenylcarbamate‐based ones more often showed a chiral recognition ability compared to cellulose phenylcarbamate derivatives. An interesting effect was observed with formic acid as additive on enantiomer resolution and enantiomer elution order for some basic drugs. Thus, for instance, the enantioseparation of several β‐blockers (atenolol, sotalol, toliprolol) improved not only by the addition of a more conventional basic additive to the mobile phase, but also by the addition of an acidic additive. Moreover, an opposite elution order of enantiomers was observed depending on the nature of the additive (basic or acidic) in the mobile phase. Chirality 27:228–234, 2015. © 2015 Wiley Periodicals, Inc.     

New data on the subgenus Harpopaederus of the genus Paederus (Coleoptera,Staphylinidae, Paederinae) of mainland China

Paederus (Harpopaederus) xui Peng & Li, sp. n. (Sichuan: Micang Shan) is described. Additional records of five Harpaederus species are reported. All of these species are illustrated.     

Thysanoptera of Bulgaria

The present checklist includes data on the species composition, geographic distribution and feeding preferences of thrips species in Bulgaria. In total, 155 species in 48 genera are listed. Of these, 125 species belong to suborder Terebrantia and include 103 species of 33 genera in family Thripidae, 14 species of two genera in Aeolothripidae, seven species of two genera in Melanthripidae and one species in Fauriellidae. In suborder Tubulifera, 30 species of 10 genera in the single family Phlaeothripidae are listed. Of the 155 Bulgarian thrips species, 87.7% are phytophagous, 4.5% are obligate predators, 5.8% are mycophagous and 1.9% are with unknown feeding preferences. Fourteen pest species are listed for Bulgaria, of which Frankliniella occidentalis, Thrips tabaci and Haplothrips tritici are of economic importance. The list provides detailed information on the horizontal and vertical distribution of Thysanoptera in 5 regions and 45 subregions of Bulgaria. The present paper also includes an evaluation of the biodiversity of Thysanoptera and the extent to which each region of the country has been studied.     

Three new species of Epicephala Meyrick (Lepidoptera,Gracillariidae) associated with Phyllanthus microcarpus (Benth.) (Phyllanthaceae)

Three new species of Epicephala Meyrick, 1880 are described based on specimens reared from fruits of Phyllanthus microcarpus (Benth.): Epicephala microcarpa sp. n. and Epicephala laeviclada sp. n. from Guangxi and Hainan, and Epicephala tertiaria sp. n. from Guangdong and Guangxi. Photographs of adults and illustrations of genital structures are provided.     

Ephemeroptera,Plecoptera, and Trichoptera on Isle Royale National Park,USA, compared to mainland species pool and size distribution

Extensive sampling for aquatic insects was conducted in the orders Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies) (EPT) of Isle Royale National Park (ISRO), Michigan, United States of America, during summer 2013. The island was ice covered until 8,000 to 10,000 years ago and is isolated by 22–70 km distance from the mainland. Two hypotheses were examined: that ISRO EPT richness would be much reduced from the mainland, and that the species colonizing ISRO would be of smaller size than mainland, adults presumably using updrafts to bridge the distance from mainland sources. Data sets were developed for known mainland EPT species and size for those species. The first hypothesis was confirmed with the mainland species pool consisting of 417 EPT, while ISRO is known to support 73 species. Richness of EPT is directly related to the number of specimens examined. Small streams supported five EPT species, while 15–25 species were found in larger streams. Lakeshores had intermediate diversity. The second hypothesis was substantiated for stoneflies, but not for mayflies or caddisflies. Stoneflies apparently are poorer fliers than either of the other two orders.     

Lamprops donghaensis sp. n. (Crustacea,Cumacea, Lampropidae), a new species from Korean waters

A new species of Cumacea belonging to the genus Lamprops Sars was collected from the East Sea of Korea. This new species resembles Lamprops comatus Zimmer, Lamprops carinatus Hart, Lamprops flavus Harada, Lamprops pumilio Zimmer, Lamprops tomalesi Gladfelter, and Lamprops obfuscatus (Gladfelter) in lacking lateral oblique ridges on the carapace and lateral setae on the telson. The new species, however, is distinguished from its congeners by having a dorsal concave groove and a lateral rounded depressed area on pereonite 2. The new species is fully illustrated and compared with related species. A key to the world Lamprops species lacking lateral ridges on the carapace is also provided.     

Checklist of tortoise beetles (Coleoptera,Chrysomelidae, Cassidinae) from Colombia with new data and description of a new species

A new tortoise beetle species, Cyrtonota abrili, is described from the Antioquia and Caldas departments in Colombia. New faunistic data are provided for 87 species, including 16 new additions to the country’s fauna. A checklist of the known 238 species of tortoise beetles recorded from Colombia is given.