Identification of the suppressive factors for human immunodeficiency virus type-1 replication using the siRNA mini-library directed against host cellular genes

We performed the screening to find the novel host factors affecting human immunodeficiency virus type-1 (HIV-1) replication using the siRNA mini-library consisted with 257 siRNAs directed against cellular genes. J111 cells, a human acute monocytic leukemia cell line, were transfected with individual siRNA, followed by either infected or transfected with the HIV-1 molecular clone with luciferase reporter gene in 96-well plate format. The results showed that six siRNAs significantly enhanced the HIV-1 replication in J111 cells, indicating that the target cellular genes of those siRNAs may negatively regulate HIV-1 replication in normal cell culture condition. We also discuss the possible mechanisms by which those cellular proteins regulate viral replication.     

The effects of environmental variables and human disturbance on woody species richness and diversity in a bamboo–deciduous forest in northeastern Thailand

Variations in species richness and diversity at a local scale are affected by a number of complex and interacting variables, including both natural environmental factors and human-made changes to the local environment. Here we identified the most important determinants of woody species richness and diversity at different growth stages (i.e. adult, sapling and seedling) in a bamboo–deciduous forest in northeast Thailand. A total of 20 environmental and human disturbance variables were used to determine the variation in species richness and diversity. In total, we identified 125 adult, 111 sapling (within fifty 20 × 20-m plots) and 89 seedling species (within one hundred and twenty 1 × 1-m subplots). Overall results from stepwise multiple regression analyses showed that environmental variables were by far the most important in explaining the variation in species richness and diversity. Forest structure (i.e. number of bamboo clumps and canopy cover) was important in determining the adult species richness and diversity (R ² = 0.48, 0.30, respectively), while topography (i.e. elevation) and human disturbance (i.e. number of tree stumps) were important in determining the sapling species richness and diversity (R ² = 0.55, 0.39, respectively). Seedling species richness and diversity were negatively related to soil phosphorus. Based on our results, we suggest that the presence of bamboos should be incorporated in management strategies for maintaining woody species richness and diversity in these forest ecosystems. Specifically, if bamboos cover the forest floor at high densities, it may be necessary to actively control these species for successful tree establishment.     

Bamboo dominance reduces tree regeneration in a disturbed tropical forest

Human disturbance may change dominance hierarchies of plant communities, and may cause substantial changes in biotic environmental conditions if the new dominant species have properties that differ from the previous dominant species. We examined the effects of bamboos (Bambusa tulda and Cephalostachyum pergracile) and their litter on the overall woody seedling abundance, species richness and diversity in a mixed deciduous forest in northeastern Thailand. These bamboo species are gaining dominance after human disturbance. Our results show that seedling abundance and species richness were reduced by bamboo canopies. Seedling abundance and species diversity under bamboo canopies were affected by bamboo litter, whereas seedling abundance and species diversity outside bamboo canopies did not respond to the mixed-tree litter manipulation. Removal of bamboo litter increased seedling abundance and species diversity. However, bamboo litter addition did not affect seedling abundance or species diversity compared to either control or litter removal. This may indicate that the effect of natural amount of bamboo litter is as high as for litter addition in preventing seedling establishment by woody species and hence in minimizing resource competition. We conclude that undergrowth bamboos and their litter affect tree seedling regeneration differently from mixed-tree litter, causing changes in plant community composition and species diversity. Increased human disturbance, causing a shift in dominance structure of these forests, may result in a concomitant reduction in their overall woody species abundance, richness and diversity. Thus, management of bamboos by controlling their distribution in areas of high bamboo density can be an important forest restoration method.     

Optimised expression in Escherichia coli and purification of the functional form of the Bacillus thuringiensis Cry4Aa delta-endotoxin

Achieving high-level expression of the Bacillus thuringiensis Cry4Aa mosquito-larvicidal protein was demonstrated. The 130-kDa Cry4Aa protoxin was overexpressed as an inclusion body in Escherichia coli under the control of the tac promoter together with the cry4Ba promoter. The solubility of the toxin inclusions in carbonate buffer, pH 10.0, was markedly enhanced at a cultivation temperature of 30 degrees C. Elimination of the tryptic cleavage site at Arg-235 in the loop between helices 5 and 6 still retained the high-level toxicity of E. coli cells expressing the Cry4Aa mutant against Aedes aegypti larvae. Trypsin digestion of the R235Q mutant protoxin produced a protease-resistant fragment of ca. 65kDa. A homogeneous product of the 65-kDa trypsin-treated R203Q protein was obtained after size-exclusion chromatography that would pave the way for the further crystallisation and X-ray crystallographic studies.     

Targeted mutagenesis of loop residues in the receptor-binding domain of the Bacillus thuringiensis Cry4Ba toxin affects larvicidal activity

Loop residues in domain II of Bacillus thuringiensis Cry delta-endotoxins have been demonstrated to be involved in insecticidal specificity. In this study, selected residues in loops beta6-beta7 (S(387)SPS(390)), beta8-beta9 (S(410), N(411), T(413), T(415), E(417) and G(418)) and beta10-beta11 (D(454)YNS(457)) in domain II of the Cry4Ba mosquito-larvicidal protein were changed individually to alanine by PCR-based directed mutagenesis. All mutant toxins were expressed in Escherichia coli JM109 cells as 130-kDa protoxins at levels comparable to the wild type. Only E. coli cells that express the P389A, S410A, E417A, Y455A or N456A mutants exhibited a loss in toxicity against Aedes aegypti mosquito larvae of approximately 30% when compared to the wild type. In addition, E. coli cells expressing double mutants, S410A/E417A or Y455A/N456A, at wild-type levels revealed a significantly higher loss in larvicidal activity of approximately 70%. Similar to the wild-type protoxin, both double mutant toxins were structurally stable upon solubilisation and trypsin activation in carbonate buffer, pH 9.0. These results indicate that S(410) and E(417) in the beta8-beta9 loop, and Y(455) and N(456) in the beta10-beta11 loop are involved in larvicidal activity of the Cry4Ba toxin.     

Crystal structure of BinB: A receptor binding component of the binary toxin from Lysinibacillus sphaericus

The binary toxin (Bin), produced by Lysinibacillus sphaericus, is composed of BinA (42 kDa) and BinB (51 kDa) proteins, which are both required for full toxicity against Culex and Anopheles mosquito larvae. Specificity of Bin toxin is determined by the binding of BinB component to a receptor present on the midgut epithelial membranes, while BinA is proposed to be a toxic component. Here, we determined the first crystal structure of the active form of BinB at a resolution of 1.75 Å. BinB possesses two distinct structural domains in its N‐ and C‐termini. The globular N‐terminal domain has a β‐trefoil scaffold which is a highly conserved architecture of some sugar binding proteins or lectins, suggesting a role of this domain in receptor‐binding. The BinB β‐rich C‐terminal domain shares similar three‐dimensional folding with aerolysin type β‐pore forming toxins, despite a low sequence identity. The BinB structure, therefore, is a new member of the aerolysin‐like toxin family, with probably similarities in the cytolytic mechanism that takes place via pore formation. Proteins 2014; 82:2703–2712. © 2014 Wiley Periodicals, Inc.     

Do disturbance and productivity influence evenness of seedling,sapling and adult tree species across a semi‐deciduous tropical forest landscape?

Disturbance and productivity may influence and alter community structure by affecting the partitioning of resources among species. Here, we examined how evenness in the relative abundance of growth stages (seedlings, saplings and adults) of woody species is related to measures of productivity (i.e. total diameter breast high (dbh) and tree volume) and aspects of human disturbance (i.e. number of tree stumps, area covered by charcoal making holes and trail length) in a bamboo‐deciduous forest, northeastern of Thailand. Our results using stepwise multiple regressions showed that productivity (total dbh) explained a significant part of the variation in evenness only at the adult stage where evenness decreased with productivity. We found a decreased evenness of saplings with the area covered by charcoal making holes. Evenness of seedlings was not related to productivity or human disturbance variables and other environmental variables contribute more to explain the variation in evenness at this stage. Evenness was correlated consistently between the growth stages but the strength of relationships diminishes across the stages. Our results suggest that high productivity and human disturbance may facilitate competitive dominant species, affecting evenness in woody communities.     

Association of the components of the binary toxin from Bacillus sphaericus in solution and with model lipid bilayers

We show herein that interaction in aqueous solution of the two components of binary toxin from Bacillus sphaericus, BinA and BinB, leads to a dramatic conformational change, from beta turns or random coil, to beta structure. Also, either BinA or BinB separately or their equimolar mixture, interact with lipid bilayers resulting in further conformational changes. Upon membrane association, the change in conformation observed for BinA or BinB separately is different from that observed when the proteins are combined, indicating that proper folding depends on the presence of the complementary subunit. We also show, in contrast to previous reports, that BinB, but not BinA, is able to insert in model neutral lipid monolayers.     

Human herpesvirus 6 variant A but not variant B induces fusion from without in a variety of human cells through a human herpesvirus 6 entry receptor,CD46

Human herpesvirus 6 (HHV-6) is a lymphotropic betaherpesvirus that productively infects T cells and monocytes. HHV-6 isolates can be differentiated into two groups, variants A and B (HHV-6A and HHV-6B). Here, we show a functional difference between HHV-6A and -6B in that HHV-6A induced syncytium formation of diverse human cells but HHV-6B did not. The syncytium formation induced by HHV-6A was observed 2 h after infection; moreover, it was found in the presence of cycloheximide, indicating that HHV-6A induced fusion from without (FFWO) in the target cells. Furthermore, the fusion event was dependent on the expression of the HHV-6 entry receptor, CD46, on the target cell membrane. In addition, we determined that short consensus repeat 2 (SCR2), -3, and -4 of the CD46 ectodomain were essential for the formation of the virus-induced syncytia. Monoclonal antibodies against glycoproteins B and H of HHV-6A inhibited the fusion event, indicating that the syncytium formation induced by HHV-6A required glycoproteins H and B. These findings suggest that FFWO, which HHV-6A induced in a variety of cell lines, may play an important role in the pathogenesis of HHV-6A, not only in lymphocytes but also in various tissues, because CD46 is expressed ubiquitously in human tissues.     

A trimeric building block model for Cry toxins in vitro ion channel formation

The crystal (Cry) insecticidal toxins, or delta-endotoxins, are lethal to a wide variety of insect larvae, and are therefore very important in insect control. Toxicity has been explained by formation of transmembrane oligomeric pores or ion channels and, more recently, by the ability of the monomeric toxin to subvert cellular signaling pathways. The structure, topology, and precise role of the putative pore in toxicity are not known. However, in vitro biophysical studies suggest that helices alpha4 and alpha5 in domain I insert into the lipid bilayer as an alpha-helical hairpin. Mutagenesis studies have assigned an important role to alpha5 in maintaining oligomerization, and to alpha4 in channel formation. To detect the possible homo-oligomerizing tendencies of these two helices, we have used the evolutionary conservation data contained in sixteen Cry homologs in order to filter non-native interactions found during a global conformational search. No conserved homo-oligomer was found for alpha4, but a right handed trimeric alpha5 model was present in the simulations of all Cry sequences. We propose a model for Cry toxin oligomerization based on sequence analysis and available mutagenesis data.