A preliminary survey for human immunodeficient virus (HIV) infections in tuberculosis and melioidosis patients in Ubon Ratchathani, Thailand.

A preliminary survey was conducted for the prevalence of HIV infections in pulmonary tuberculosis and melioidosis patients in Ubon Ratchathani province, in Thailand, the second largest province in population which supplies labors to Bangkok metropolis. In this province, tuberculosis is prevalent in a higher rate than in most other provinces and melioidosis is endemic. Four HIV-seropositives were found in a total of 551 suspected and culture-positive cases of pulmonary tuberculosis, while no HIV-seropositive was found in 121 melioidosis patients. In view of the rapidly expanding HIV-infections in Thailand, a strict watch will be needed on the future epidemiological status of HIV-infection in tuberculous patient.     

Dynamics of the protein structure of T169S pyranose 2‐oxidase in solution: Molecular dynamics simulation

Pyranose 2‐oxidase (P2O) from Trametes multicolor contains FAD as cofactor, and forms a tetramer. The protein structure of a mutated P2O, T169S (Thr169 is replaced by Ser), in solution was studied by means of molecular dynamics simulation and analyses of photoinduced electron transfer (ET) from Trp168 to excited isoalloxazine (Iso*), and was compared with wild type (WT) P2O. Hydrogen bonding between Iso and nearby amino acids was very similar as between T169S and WT protein. Distances between Iso and Tyr456 were extremely heterogeneous among the subunits, 1.7 (1.5 in WT) in subunit A (Sub A), 0.97 (2.2 in WT) in Sub B, 1.3 (2.1 in WT) in Sub C, 1.3 nm (2.0 in WT) in Sub D. Mean values of root of mean square fluctuation over all residues were greater by four times than those in WT. This suggests that the protein structure of T169S is much more flexible than that of WT. Electrostatic (ES) energies between Iso anion in one subunit and ionic groups in the entire protein were evaluated. It was found that more than 50% of the total ES energy in each subunit is contributed from other subunits. Reported fluorescence decays were analyzed by a method as WT, previously reported. Electron affinities of Iso* in T169S were appreciably higher than those in WT. Static dielectric constants near Iso and Trp168 were also quite higher in T169S than those in WT.     

The C-terminal region of xylanase domain in Xyn11A from Paenibacillus curdlanolyticus B-6 plays an important role in structural stability

Paenibacillus curdlanolyticus B-6 produces an extracellular multienzyme complex containing a major xylanase subunit, designated Xyn11A, which includes two functional domains belonging to glycosyl hydrolase family-11 (GH11) and carbohydrate binding module family-36 (CBM36) and possesses a glycine and asparagine-rich linker (linker). To clarify the roles of each functional domain, recombinant proteins XynXL and XynX (CBM36 deleted and CBM36 and linker deleted, respectively) were constructed. Their xylanase activities were similar toward soluble xylan, whereas XynXL showed decreased hydrolysis activity toward insoluble xylan while XynX had no xylanase activity. To determine the significance of the linker and its neighbor region, XynX was subjected to secondary structural alignments using circular dichroism (CD) spectroscopy and three-dimensional (3D) structural analysis. A seven amino acid (NTITIGG) neighbor linker sequence was highly conserved among GH11 xylanases of Paenibacillus species. Although XynX exhibited a typical GH11 xylanase structure, conformational gaps were observed in the β6- and β12-sheets and in CD spectra. Flipping of the Arg163 side chains in the subsite was also observed upon analysis of superimposed models. Docking analysis using xylohexaose indicated that flipping of the Arg163 side chains markedly affected substrate binding in the subsite. To identify the amino acids related to stabilizing the substrate binding site, XynX with an extended C-terminal region was designed. At least seven amino acids were necessary to recover substrate binding and xylanase activity. These results indicated that the seven amino acid neighbor Xyn11A linker plays an important role in the activity and conformational stability of the xylanase domain.     

Three new species of the carnivorous snail genus Perrottetia Kobelt, 1905 from Thailand (Pulmonata,?Streptaxidae)

Three new species of the streptaxid snail genus Perrottetia are described from north and northeastern Thailand, Perrottetia aquilonaria sp. n., Perrottetia dermapyrrhosa sp. n. and Perrottetia phuphamanensis sp. n. Each species is endemic to a single or a few limestone mountain ranges. The species are characterized by the morphology of their genital organs, as well as by shell characters. Perrottetia aquilonaria sp. n. has a club shaped distal penis and large penial hooks are present and penial papillae cover almost the entire penial hook portion; adjacent areas possess low reticulated folds. Perrottetia dermapyrrhosa sp. n. has a long genital atrium and the penial sheath is about two-thirds of the penis length. Penial hooks are long, scattered and sunken into deep ovate hollows; vaginal hooks are present. Perrottetia phuphamanensis sp. n. has a rounded and protruded shell periphery. The aperture is subcircular, peristome is thick and the second parietal lamella is adjacent to the first parietal lamella; a basal lamella is the smaller than in the other Thai species.     

Structural and Dynamical Properties of a Full-length HIV-1 Integrase: Molecular Dynamics Simulations

Abstract

The structural and dynamical properties of the complete full-length structure of HIV-1 integrase were investigated using Molecular Dynamics approach. Simulations were carried out for the three systems, core domain only (CORE), full-length structure without (FULL) and with a Mg²⁺ (FULL+ION) in its active site, aimed to investigate the difference in the molecular properties of the full-length models due to their different construction procedures as well as the effects of the two ends, C- and N-terminal, on those properties in the core domain. The full-length structure was prepared from the two experimental structures of two-domain fragment. The following properties were observed to differ significantly from the previous reports: (i) relative topology formed by an angle between the three domains; (ii) the cavity size defined by the catalytic triad, Asp64, Asp116, and Glul52; (iii) distances and solvation of the Mg²⁺; and (iv) conformation of the catalytic residues. In addition, the presence of the two terminal domains decreases the mobility of the central core domain significantly.     

Tubeufia asiana, the teleomorph of Aquaphila albicans in the tubeufiaceae, pleosporales, based on cultural and molecular data

The teleomorph of Aquaphila albicans was discovered on submerged wood collected in Thailand. Its black, soft-textured, setose ascomata, bitunicate asci and hyaline to pale brown, multiseptate ascospores indicated an affinity to Tubeufiaceae (Dothideomycetes). After morphological or molecular comparisons with related species in Tubeufia, Acanthostigma and Taphrophila, it is described and illustrated as a new species, T. asiana Sivichai & K.M. Tsui, sp. nov. Finding this Tubeufia teleomorph was surprising, given the falcate conidia of its A. albicans anamorph, which superficially resemble the conidia of Fusarium and not the coiled, helicosporous conidia of other species in Tubeufiaceae. We assessed the phylogenetic relationships of A. albicans-T. asiana with ribosomal sequences from SSU and ITS and partial LSU regions by parsimony and Bayesian analysis. An initial set of 40 taxa representing a wide range of ascomycete families and their SSU sequences from GenBank showed A. albicans-T. asiana to be nested within the Tubeufiaceae with 100% bootstrap support. Their placement was inferred with ITS and partial LSU ribosomal sequences. The nearly identical ITS sequences of two isolates of A. albicans and one isolate of Tubeufia asiana united these fungi as a monophyletic group with 100% bootstrap support and further nested them, with 88% bootstrap support, in a clade containing Helicoon gigantisporum and Helicoma chlamydosporum. This is the first molecular phylogenetic study to place a nonhelicosporous species within the Tubeufiaceae and to show that helical conidia were lost at least once within the family.     

Stone-tool usage by Thai long-tailed macaques (Macaca fascicularis)

In January and March of 2005, we conducted surveys of long-tailed macaques at Piak Nam Yai Island, Laem Son National Park (9 degrees N 34-35', 98 degrees E 28'), Ranong Province, situated in southern Thailand. Two of the three troops of long-tailed macaques found on the island were observed using axe-shaped stones to crack rock oysters, detached gastropods (Thais tissoti, Petit, 1852), bivalves (Gafrarium divaricatum, Gmelin, 1791), and swimming crabs (Thalamita danae, Stimpson, 1858). They smashed the shells with stones that were held in either the left or right hand, while using the opposite hand to gather the oyster meat. Some monkeys used both hands to handle the stones. According to Matsuzawa's 1996 hierarchical classification of tool usage (levels 0-3), the tool usage by Thai long-tailed macaques could be characterized as either level 1 (cracking rock oysters with stones) or level 2 (cracking drifting mollusks and crabs with stones by placing them on a rock). Our discovery of stone-tool usage by Thai long-tailed macaques provides a new point of reference for discussions regarding the evolution of tool usage and the material culture of primates.