Homology modeling and molecular dynamics simulations of Dengue virus NS2B/NS3 protease: insight into molecular interaction

The pathogenic West Nile virus (WNV) and Dengue virus (DV) are growing global threats for which there are no specific treatments. Both viruses possess a two component NS2B/NS3 protease which cleaves viral precursor proteins. Whereas for the WNV protease two crystal structures in complex with an inhibitor have been solved recently, no such information is available for the DV protease. Here, we report the generation of a homology model of DV NS2B/NS3 protease. Since it is known from the related WNV protease that it adopts a distinct conformation in free and in inhibitor‐complexed form, a special emphasis was given to the analysis of the protease flexibility. Therefore, several models of DV NS2B/NS3 protease complexed with the peptidic inhibitor (Bz‐Nle(P4)‐Lys(P3)‐Arg(P2)‐Arg(P1)‐H) were generated. The first DV protease model (DV‐1) was constructed using the available crystal structure of the apo DV NS2B/NS3 protease. The second model (DV‐2) was built taking the WNV NS3/NS2B protease in the inhibitor‐complexed form as the template structure. Molecular dynamics simulations which were carried out for the WNV crystal structures as well as for the DV models provided an understanding of the role of NS2B for maintaining the protease in the active conformation. It was also demonstrated that NS2B is not only important for maintaining NS3 in the active form, but is also essential for establishing the interaction between residues from the S2 pocket and the peptidic inhibitor. The DV NS2B/NS3 model in the productive conformation can now be used for structure‐based design purposes. Copyright © 2009 John Wiley & Sons, Ltd.     

Pyranocoumarins from the twigs of Mammea siamensis

Four unusual pyranocoumarins (1-4) have been isolated from the dried twigs of M. siamensis. The structures were determined by spectroscopic data, especially 1D and 2D NMR experiments.     

Biochemical assessment of the taxonomic diversity of the operculate land snail, Cyclophorus fulguratus (Gastropoda: Cyclophoridae), from Thailand

Allozyme variation was examined in 223 samples of the operculate land snail Cyclophorus fulguratus from 13 localities across three regions of Thailand. Using horizontal starch gel electrophoresis, 13 allozyme presumed loci (12 polymorphic) were screened. Heterozygosity was moderate in C. fulguratus (H_exp = 0.008–0.127) with a high genetic heterogeneity among samples (F_st = 0.734). Populations showed a greater genetic differentiation in central Thailand (F_st = 0.380) than in northeastern Thailand (F_st = 0.108), suggesting frequent gene flow among populations in northeastern Thailand. C. fulguratus exhibits a strong pattern of isolation by distance over the entire tested species range in Thailand and may potentially have been involved in an extensive local fragmentation. Results of the distance analysis revealed that large genetic divergence has occurred among the central, northeastern and eastern Thailand groups [D = 0.361–0.701], strongly suggesting populations from these three geographical regions may actually represent or else be evolving into separate species.     

Cytotoxic and antiplasmodial substances from marine-derived fungi, Nodulisporium sp. and CRI247-01

Nodulisporacid A (1) was isolated from a marine-derived fungus Nodulisporium sp. CRIF1, while vermelhotin (5) was obtained from an unidentified fungus CRI247-01 (a member of the Order Pleosporales). Both 1 and 5 occurred as equilibrium E/Z mixtures. Ester derivatives (2 and 3) and vermelhotin (5) showed cytotoxic activity against eleven cancer cell lines. Nodulisporacid A (1) and vermelhotin (5) exhibited moderate antiplasmodial activity.     

A suspected new species of Leishmania, the causative agent of visceral leishmaniasis in a Thai patient

A suspected new species of Leishmania is described as the causative agent of the third reported case of autochthonous visceral leishmaniasis in a Thai man living in Southern Thailand. The results of PCR-restriction fragment length polymorphism and sequence analysis of the internal transcribed spacer 1 of ssrRNA and the mini-exon genes were different from those of previously reported Leishmania species. A direct agglutination test (DAT) revealed that antibody against Leishmania infection was detected in nine domestic cats. No potential vectors could be identified. A large-scale epidemiological survey of leishmaniasis should be urgently conducted since visceral leishmaniasis is considered an emerging disease of public health concern in Thailand.     

Taxonomic revision of the Elephant Pupinid snail genus Pollicaria Gould, 1856 (Prosobranchia,Pupinidae)

The status of species currently assigned to the Southeast Asian Elephant Pupinid snail genus Pollicaria Gould, 1856 is reassessed. Shell, radular and reproductive morphology are investigated and analysed with reference to karyotype patterns previously reported and to distribution patterns among the species. Six previously described species are recognised: Pollicaria gravida (Benson, 1856), Pollicaria myersii (Haines, 1855), Pollicaria mouhoti (Pfeiffer, 1862), Pollicaria elephas (Morgan, 1885), Pollicaria crossei (Dautzenberg & d’Hamonville, 1887) and Pollicaria rochebruni (Mabille, 1887). A new subspecies, Pollicaria mouhoti monochroma ssp. n.,is proposed and a dichotomous key to species is provided.     

The millipede genus Tetracentrosternus Pocock, 1895 (Polydesmida,Paradoxosomatidae, Alogolykinae,Alogolykini), with a description of the first,new species from Thailand

The millipede subfamily Alogolykinae and the tribe Alogolykini are recorded in Thailand for the first time,being represented there by Tetracentrosternus theelorsuensis sp. n. While the new species has characteristics that place it in the genus Tetracentrosternus, it also shows a number of unique features that make it necessary to rediagnose this Oriental genus, as well as to key its three currently known species and map their distributions. The tribes Alogolykini and Polydrepanini, as well as the subfamily Alogolykinae are also briefly redefined.     

Unusual glycosides of pyrrole alkaloid and 4'-hydroxyphenylethanamide from leaves of Moringa oleifera

Glycosides of pyrrole alkaloid (pyrrolemarumine 4″-O-α-l-rhamnopyranoside) and 4′-hydroxyphenylethanamide (marumosides A and B) were isolated from leaves of Moringa oleifera along with eight known compounds; niazirin, methyl 4-(α-l-rhamnopyranosyloxy)benzylcarbamate, benzyl β-d-glucopyranoside, benzyl β-d-xylopyranosyl-(1 → 6)-β-d-glucopyranoside, kaempferol 3-O-β-d-glucopyranoside, quercetin 3-O-β-d-glucopyranoside, adenosine and l-tryptophan. Structure elucidations were based on analyses of chemical and spectroscopic data including 1D- and 2D-NMR.     

Systematics of the freshwater leech genus Hirudinaria Whitman, 1886 (Arhynchobdellida,Hirudinidae) from northeastern Thailand

In total, 435 specimens of the Southeast Asian freshwater leech species within the Hirudinidae family were collected from 17 locations of various types of aquatic habitats in northeastern Thailand. They were all morphologically placed within the genus Hirudinaria Whitman, 1886 and there were three distinct species: the common Hirudinaria manillensis, 78.2% of all collected specimens and at all 17 locations, Hirudinaria javanica at 20.3% of collected samples and from five locations and a rarer unidentified morphospecies (Hirudinaria sp.) with six samples from only two locations. The karyotypes of these three species were examined across their range in this study area for 38, 11 and 6 adult specimens of Hirudinaria manillensis, Hirudinaria javanica and Hirudinaria sp., respectively. This revealed different chromosome numbers among all three species, with Hirudinaria javanica having n = 13, 2n = 26, Hirudinaria manillensis lacked one small chromosome pair with n = 12, 2n = 24, and the unknown Hirudinaria sp. differed from any known Hirudinaria karyotypes in exhibiting a higher chromosome number (n = 14, 2n = 28) and a gradual change in size from large to small chromosomes. This suggests that the unknown Hirudinaria sp. is a new biological species. However, phylogenetic analysis based upon a 658 bp fragment of the cytochrome oxidase subunit I gene placed this unknown morphospecies within the Hirudinaria manillensis clade, perhaps then suggesting a recent sympatric speciation, although this requires further confirmation. Regardless, the chromosomes of all three species were asymmetric, most with telocentric elements. A distinct bi-armed chromosome marker was present on the first chromosome pair in Hirudinaria javanica, whilst it was on pairs 1, 2, 3 and 5 in Hirudinaria manillensis, and on pairs 3 and 5 for the unknown Hirudinaria sp.     

Bioaccumulation of heavy metals in local edible plants near a municipal landfill and the related human health risk assessment

ABSTRACT

The increase in municipal solid waste generation, along with high concentrations of heavy metals in environments near municipal landfill, has led to human health hazards. This study investigated heavy metal contamination in water, sediment, and edible plants near a municipal landfill, including the bioaccumulation factor (BAF) and potential health risks. The heavy metal concentrations in the samples were analyzed using inductively coupled plasma optical emission spectrometry (ICP-OES). The concentrations of arsenic (As), lead (Pb), cadmium (Cd), and chromium (Cr) in water samples were not detected (ND), ND, 0.006 ± 0.01 mg/L, and ND, respectively, and in sediment samples, the concentrations were 1.19 ± 0.44, 3.20 ± 0.62, 0.46 ± 0.21, and 6.97 ± 0.34 mg/kg, respectively. The highest concentrations of As (5.03 ± 0.38), Pb (1.81 ± 0.37), and Cd (1.93 ± 0.13) were found in Marsilea crenata, whereas that of Cr (5.68 ± 0.79) was detected in Ipomoea aquatica. The Cr concentration in all plant species exceeded the standard for vegetables. The BAF values followed the heavy metal concentrations. All plant species have a low potential for accumulating Pb and Cr. The edible plants in this study area might cause health hazards to consumers from As, Pb, and Cd contamination.