Molecular Variation in the Paragonimus heterotremus Complex in Thailand and Myanmar

Paragonimiasis is an important food-borne parasitic zoonosis caused by infection with lung flukes of the genus Paragonimus. Of the 7 members of the genus known in Thailand until recently, only P. heterotremus has been confirmed as causing human disease. An 8th species, P. pseudoheterotremus, has recently been proposed from Thailand, and has been found in humans. Molecular data place this species as a sister species to P. heterotremus, and it is likely that P. pseudoheterotremus is not specifically distinct from P. heterotremus. In this study, we collected metacercariae of both nominal species (identification based on metacercarial morphology) from freshwater crabs from Phetchabun Province in northern Thailand, Saraburi Province in central Thailand, and Surat Thani Province in southern Thailand. In addition, we purchased freshwater crabs imported from Myanmar at Myawaddy Province, western Thailand, close to the Myanmar-Thailand border. The DNAs extracted from excysted metacercariae were PCR-amplified and sequenced for ITS2 and cox1 genes. The ITS2 sequences were nearly identical among all samples (99-100%). Phylogenies inferred from all available partial cox1 sequences contained several clusters. Sequences from Indian P. heterotremus formed a sister group to sequences from P. pseudoheterotremus-type metacercariae. Sequences of P. heterotremus from Thailand, Vietnam, and China formed a separate distinct clade. One metacercaria from Phitsanulok Province was distinct from all others. There is clearly considerable genetic variation in the P. heterotremus complex in Thailand and the form referred to as P. pseudoheterotremus is widely distributed in Thailand and the Thai-Myanmar border region.     

Molecular data reveal cryptic lineages within the northeastern Atlantic and Mediterranean small mussel drills of the Ocinebrina edwardsii complex (Mollusca: Gastropoda: Muricidae)

We used a molecular phylogenetic approach to investigate species delimitations and diversification in the mussel drills of the Ocinebrina edwardsii complex by means of a combination of nuclear (internal transcribed spacer 2, ITS2) and mitochondrial [cytochrome oxidase subunit I (COI) and 16S] sequences. Our sample included 243 specimens ascribed to seven currently accepted species from 51 sites. Five of the samples were from either the type locality of a nominal species or a close nearby locality (O. edwardsii from Corsica, O. carmelae and O. piantonii from the Kerkennah Islands, O. hispidula from the Gulf of Gabès and O. leukos from the Canary Islands), one from the inferred original locality (O. ingloria from Venice Lagoon), and specimens assigned in the recent literature to O. nicolai. We used a combination of distance‐ and tree‐based species delimitation methods to identify Molecular Operational Taxonomic Units (MOTUs) to compare with the a priori species identifications. The consensus tree obtained by BEAST on the COI alignment allows the recognition of several distinct clades supported by the three species delimitation methods employed. The eight‐MOTUs scenario, shared by the Automatic Barcode Gap Discovery (ABGD) and Generalized Mixed Yule‐Coalescent (GMYC) methods, comprises the following major clades: clade A contains the south Tunisian species Ocinebrina piantonii Cecalupo, Buzzurro & Mariani from which the sympatric taxon O. carmelae Cecalupo, Buzzurro & Mariani (new synonym) cannot be separated; clades B and C bring together all populations from the Aegean Sea and some from the Ionian Sea, respectively; clade D groups, on the one hand, the south Tunisian samples morphologically assigned to O. hispidula Pallary and, on the other, Atlantic and Alboran Sea samples (including the Canarian taxon O. leukos Houart); clade E includes a sample from the type locality of O. edwardsii and several samples from the Tyrrhenian Sea; clades F and G correspond to a few samples from the Venice Lagoon and the Tyrrhenian Sea, respectively; clade H groups the bulk of samples from the Adriatic Sea, including samples from the Venice Lagoon morphologically identified as Ocinebrina ingloria (Crosse), and some from the Ionian Sea. No final conclusions could be reached to reconcile the currently recognized morphological taxa with the clades suggested by the COI data. The geographical structure proposed by the mitochondrial markers is similar to that found in other marine invertebrates and partially corresponds to the species defined by shell characters. We propose here a framework for the revision of the Ocinebrina edwardsii species complex, suggesting a geographical pattern for the diversification of this group in the studied area. © 2013 The Linnean Society of London     

Growth of Geobacter sulfurreducens on Poorly Crystalline Fe(III) Oxyhydroxide Coatings

Few studies have examined the molecular to micron-scale interactions between dissimilatory Fe(III)-reducing bacteria and poorly crystalline Fe(III) phases which are frequently the most bioavailable Fe(III) sources in the subsurface. Here we describe methods for analysing these interactions using a range of chemical and spectroscopic techniques. Glass slides were coated with a synthetic poorly crystalline Fe(III) phase and then incubated in the presence of the Fe(III)-reducing bacterium Geobacter sulfurreducens and a suitable growth medium. Growth on the Fe(III)-coating was observed via cell staining and environmental scanning electron microscopy while microbial Fe(III) reduction was quantified using a colorimetric assay. However, following microbial reduction, Fe(II) could not be detected on the slide surface using X-ray photoelectron spectroscopy. Fe(II)-coated control slides showed that the mineral surface was not re-oxidised during handling or analysis. Further experiments intended to demonstrate removal of Tc(VII) and Cr(VI) from solution via abiotic reduction mediated by biogenic Fe(II) on the slide surface resulted in far lower levels of Tc(VII) and Cr(VI) reduction than expected. These data may indicate that the electrons transferred from G. sulfurreducens to poorly crystalline Fe(III) involves the deeper mineral structure, so that Fe(II) phases are not detectable on the surface. The environmental implications of this hypothesis are discussed.     

Morphological and genetic relationship of two closely‐related giant water bugs: Appasus japonicus Vuillefroy and Appasus major Esaki (Heteroptera: Belostomatidae)

The East Asian giant water bug species Appasus japonicus Vuillefroy and Appasus major Esaki are aquatic hemipteran insects whose ranges overlap, particularly in the Japanese Archipelago and on the Korean Peninsula. In rare cases, the two species co‐occur. Furthermore, they are very similar ecologically and also morphologically, making their identification extremely difficult, and the possibility of hybridization has also been suggested. In the present study, we re‐examined their taxonomic validity, and the characteristics useful for identifying them. To re‐examine the morphological traits useful for distinguishing these two species, 222 specimens of A. japonicus collected from Japan, Korea, and China, and 132 specimens of A. major from Japan and Korea, were examined. We also performed molecular phylogenetic analyses based on the mitochondrial DNA 16S rRNA and cytochrome oxidase subunit I (COI) regions and the nuclear DNA Histone 3 region. Although the two species are very similar ecologically and also morphologically, they showed significant genetic differentiation. Thus, there is likely some form of reproductive isolation acting between them. Major morphological characteristics overlap extensively between A. japonicus and A. major, and no particular trait was identified as being effective for differentiating these species. All the morphological characteristics examined overlapped between A. japonicus and A. major. However, a principal component analysis based on all of the morphological characteristics revealed that, despite the overlap between these species, it was possible to morphologically distinguish them. Therefore, a more accurate identification becomes possible using multiple characteristics rather than a single characteristic. The male genital paralobes, evaluated as the most useful morphological characteristic, was effective with 100% probability for the Japanese Appasus species. However, for the Asian (i.e. Korean) specimens, this characteristic was not useful. On the other hand, the results of molecular phylogenetic analyses based on the mitochondrial DNA 16S rRNA and COI regions and the nuclear DNA Histone 3 region clearly showed significant genetic differentiation between the two species. Notably, the results for the mitochondrial COI region strongly supported the independence of each monophyletic group (i.e. validity of each species). Therefore, DNA barcoding based on the mitochondrial DNA COI region is also considered useful for the identification of A. japonicus and A. major. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 615–643.     

Phylogeographic pattern and regional evolutionary history of the maize stalk borer Busseola fusca (Fuller) (Lepidoptera: Noctuidae) in sub-Saharan Africa

Busseola fusca (Fuller) (Lepidoptera: Noctuidae) is one of the major cereal pests in sub-Saharan Africa. Previous phylogeographic investigations on samples collected in Kenya, Cameroon and West-Africa showed the presence of three main clades (W, KI, KII) originated from populations isolated in West and East Africa around one million years ago. Demographic and phylogenetic analyses suggested that this event was followed by local demographic expansion and isolation by distance. These hypotheses were tested by a more comprehensive sampling across B. fusca’s geographic range in Africa. Comparisons of sequences of partial mitochondrial DNA gene (cytochrome b) from 489 individuals of 98 localities in southern, central, eastern and western African countries confirmed the presence of the three main clades. Phylogenetic, F-statistics, demographic parameters and nested clade phylogeographic analyses confirmed that the clades experienced geographic and demographic expansion with isolation by distance after their isolation in three refuge areas. The geographic range of clade KII, already known from East to Central sub-Saharan Africa was extended to Southern Africa. Mismatch distribution analysis and the negative values of Tajima’s D index are consistent with a demographic expansion hypothesis for these three clades. Significant genetic differentiations were revealed at various hierarchical levels by analysis of molecular variance (AMOVA). Hypotheses about the geographic origin of the three main clades are detailed.     

Integrating cell‐free biosyntheses of heme prosthetic group and apoenzyme for the synthesis of functional P450 monooxygenase

Harnessing the isolated protein synthesis machinery, cell‐free protein synthesis reproduces the cellular process of decoding genetic information in artificially controlled environments. More often than not, however, generation of functional proteins requires more than simple translation of genetic sequences. For instance, many of the industrially important enzymes require non‐protein prosthetic groups for biological activity. Herein, we report the complete cell‐free biogenesis of a heme prosthetic group and its integration with concurrent apoenzyme synthesis for the production of functional P450 monooxygenase. Step reactions required for the syntheses of apoenzyme and the prosthetic group have been designed so that these two separate pathways take place in the same reaction mixture, being insulated from each other. Combined pathways for the synthesis of functional P450 monooxygenase were then further integrated with in situ assay reactions to enable real‐time measurement of enzymatic activity during its synthesis. Biotechnol. Bioeng. 2013; 110: 1193–1200. © 2012 Wiley Periodicals, Inc.     

Hagfish phylogeny and taxonomy,with description of the new genus Rubicundus (Craniata,Myxinidae)

A recent phylogenetic analysis of the Myxinidae based on the 16S rRNA gene resulted in synonymization of Paramyxine with Eptatretus. This created homonymy of Paramyxine fernholmi with Eptatretus fernholmi and Paramyxine wisneri with Eptatretus wisneri. In order to resolve this nomenclatural dilemma, we made a more extensive phylogenetic assessment of the Myxinidae and examined the nomenclature of the family. We used 75 sequences (37 of which new for this study) of a 561 bp fragment of the 16S rRNA gene, representing 33 species, and 72 sequences (37 of which new for this study) of a 687 bp fragment of the cytochrome c oxidase subunit I (COI) gene, representing 23 species, to reconstruct the phylogeny of Myxinidae. The monophyly of the subfamily Myxininae, traditionally characterized by having a single pair of external gill openings, was rejected (0.50 Bayesian posterior probability) by the 16S analysis, but supported by the COI and combined COI+16S analyses (0.99 and 0.81 Bpp, respectively). The monophyly of the subfamily Eptatretinae, characterized by having several pairs of external gill openings, was not supported by the 16S analysis and rejected by the COI and combined COI+16S analysis due to the placement of Eptatretus lopheliae as the earliest branch of Myxinidae (0.71 and 0.57 Bpp, respectively). Eptatretus lopheliae and Eptatretus rubicundus formed a monophyletic group and were allocated to a new genus, Rubicundus, characterized by the presence of an elongated tubular nostril and reddish coloration. A new monotypic subfamily, Rubicundinae, was proposed for Rubicundus. The synonymy of the genera Paramyxine and Quadratus with Eptatretus was confirmed. E. fernholmi is renamed Eptatretus luzonicus. Eptatretus wisneri was renamed Eptatretus bobwisneri. Petromyzon cirrhatus Forster, 1801, Homea banksii Fleming, 1822, and Bdellostoma forsteri Müller, 1836 are synonyms, but no type specimens are known to exist. Petromyzon cirrhatus was designated as type species of Eptatretus, conserving present usage. Gastrobranchus dombeyi Shaw, 1804 has priority over other names for Chilean myxinids. Bdellostoma stoutii was designated as type species of Polistotrema Gill. The validity of the Western Atlantic Myxine limosa as distinct from the Eastern Atlantic Myxine glutinosa was confirmed.     

Mutagen Formation in the Reaction of Nitrite with the Food Components Analogous to Sorbic Acid

Mutagen formation by the reaction of sodium nitrite with some sorbic acid analogs was investigated by using the microbial mutagenicity tests (rec-assay and Ames test) together with chemical examination using TLC, and it became clear that the conjugated dienoic carbonyl structure is essential for mutagen formation by the reaction with nitrite By a large scale reaction of sodium nitrite with sorbic acid methyl ester, 5-nitro-2,4-hexadienoic acid methyl ester and ethylnitrohc acid were isolated and identified as the mam mutagens The results led to the assumption that a nitro group adjacent to the double bond is an important factor to develop mutagenicity     

A Novel Type of D-Mannitol Dehydrogenase from Acetobacter xylinum: Occurrence,Purification, and Basic Properties

We purified a novel type of D-mannitol dehydrogenase, which contains a c-type cytochrome and an unknown chromophore in the soluble fraction of an acetic acid bacterium, Acetobacter xylinum KU-1, to homogeneity. The enzyme showed the maximum activity at pH 5 and 40°C. It was stable up to 60°C at pH 6, and was inhibited by Hg²⁺ and p-quinone (K_i = 0.18 mm). The molecular weight of the enzyme was about 140,000, and those of the subunits were 69,000, 51,000, and 20,000; the enzyme is hetero-trimeric and contained 8 g-atoms of Fe per mole. The α-helix content was estimated to be about 52.9%. The enzyme catalyzed phenazine methosulfate dependent oxidation of d-mannitol with an apparent K_m of 98 μm (for d-mannitol) and V_max of 213 μmol/min/mg. The reduced form of the enzyme showed the absorption maxima at 386, 416, 480, 518, 550, and 586 nm, which are attributable to a c-type cytochrome in the enzyme.     

Partial Purification and Some Properties of ADP-glucose Phosphorylase from Potato Tubers

ADP-glucose phosphorylase [adenosine diphosphate glucose: orthophosphate adenyl- yltransferase; Dankert et ah, Biochim. Biophys. Acta, 81, 78 (1964)] was found to be widely distributed in plant tissues. The enzyme was purified 570-fold in a 24% yield from cell- free extract of growing tubers of potato (Solanum tuberosum L.). The following reaction catalyzed by the purified enzyme was found to proceed stoichiometrically. ADP-glucose +P₁→ADP+glucose-1-P

Maximal activity was observed at pH 8. The enzyme was the most stable at pH 7, showing 50% loss of its original activity after 50 min heating at 57°C. The following kinetic parameters were obtained: activation energy, 11.1 kcal/mole; Km (P₁), 2.5 mm; Km (ADP-glucose), 0.05 mm. The enzyme did not act on GDP-mannose, GDP-glucose and UDP-glucose. Neither activator nor inhibitor was found among various phosphorylated metabolites tested. The enzyme was inhibited by metal-binding reagents, EDTA and o-phenanthroline. None of the metal ions tested was found to recover the activity of chelator-treated enzyme.