Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi

Background  

Wolbachia (wBm) is an obligate endosymbiotic bacterium of Brugia malayi, a parasitic filarial nematode of humans and one of the causative agents of lymphatic filariasis. There is a pressing need for new drugs against filarial parasites, such as B. malayi. As wBm is required for B. malayi development and fertility, targeting wBm is a promising approach. However, the lifecycle of neither B. malayi nor wBm can be maintained in vitro. To facilitate selection of potential drug targets we computationally ranked the wBm genome based on confidence that a particular gene is essential for the survival of the bacterium.     

Oxidant driven signaling pathways during diabetes: role of Rac1 and modulation of protein kinase activity in mouse urinary bladder

BACKGROUND: Urinary bladder dysfunction is a complication in diabetes but the mechanisms involved are undefined. Here, we investigated roles of oxidative stress and oxidant driven signaling pathways in a murine model of diabetes, with an emphasis on urothelial vs. smooth muscle regional changes. METHODS: Mice were dosed with streptozotocin (150 mg/kg) or vehicle and studied at 5 weeks. Functional changes were assessed by in vitro cystometry. Immunohistochemical methods and automated digital imaging was used for morphometric and histochemical analysis of bladder tissue regions. RESULTS: We detected significant increases in protein 3-nitrotyrosine in both urothelium and smooth muscle regions during diabetes, demonstrating an increased prevalence of reactive nitrogen species. In light of nitric oxide synthase (NOS) isoforms as potential contributors to increased protein nitration, all three NOS isoforms were studied; region specific increases in NOS1 (urothelium and smooth muscle), NOS2 (urothelium only) but no alterations in NOS3 isoform were detected during diabetes. In contrast, p21-Rac1 (coordinating protein of NADPH oxidase) was significantly increased only in smooth muscle (diabetic vs. controls). We also investigated phosphorylation of ERK, JNK, p38 and Akt using immunohistochemical techniques; each of these was increased during diabetes but with different distributions in the two major regions of bladder tissues viz the smooth muscle and urothelium. CONCLUSIONS: The STZ mouse model of diabetes exhibits bladder dysfunction and structural changes similar to human. Reactive nitrogen species formation occurs in this setting and region specific assessments also revealed that urothelial changes and smooth muscle changes are discrete with respect to mechanisms of reactive nitrogen species (increased production of NO vs. superoxide anion) and activation of oxidant related stress signaling pathways.     

Short-term effects of nitrogen availability on wood formation and fibre properties in hybrid poplar

The application of nitrogen-containing fertilisers is one approach used to increase growth rates and productivity of forest tree plantations. However, the effects of nitrogen fertilisation on wood properties have not been systematically assessed. The aim of this work was to document the impacts of nitrogen fertilisation on wood formation and secondary xylem fibre properties. We used three fertilisation treatments in which the level of ammonium nitrate was adjusted to 0, 1 and 10 mM in a complete nutrient solution applied daily over a period of 28 days in standardised greenhouse experiments with clonal material of Populus trichocarpa (Torr and Gray) × deltoides (Bartr. ex Marsh). We showed that there was a short-term and repeatable response in which xylem fibre morphology and secondary cell wall structure adapt to a shift in N availability. Under high-nitrogen exposure, xylem fibres were 17% wider and 18% shorter compared to the adequate nitrogen treatment. A very significant thickening of the fibre cell walls was also observed throughout the stem of trees receiving the high-N treatment. It appeared that cell wall structure was greatly affected by the high-N treatment as fibres developed a modified inner cell wall layer. Histological observations indicated that the internal cell wall layer was enriched in cellulose and chemical determinations showed that wood contained more holocellulose. Together, these results indicate that the response of poplar to nitrogen availability may involve marked effects on secondary xylem formation.     

Studies on the binding site of the galactose-specific agglutinin PA-IL from Pseudomonas aeruginosa

The binding properties of Pseudomonas aeruginosa agglutinin-I (PA-IL) with glycoproteins (gps) and polysaccharides were studied by both the biotin/avidin-mediated microtiter plate lectin-binding assay and the inhibition of agglutinin-glycan interaction with sugar ligands. Among 36 glycans tested for binding, PA-IL reacted best with two glycoproteins containing Galalpha1-->4Gal determinants and a human blood group ABO precursor equivalent gp, but this lectin reacted weakly or not at all with A and H active gps or sialylated gps. Among the mammalian disaccharides tested by the inhibition assay, the human blood group Pkactive Galalpha1-->4Gal, was the best. It was 7.4-fold less active than melibiose (Galalpha1-->6Glc). PA-IL has a preference for the alpha-anomer in decreasing order as follows: Galalpha1-->6 >Galalpha1-->4 >Galalpha1-->3. Of the monosaccharides studied, the phenylbeta derivatives of Gal were much better inhibitors than the methylbeta derivative, while only an insignificant difference was found between the Galalpha anomer of methyl- and p -NO2-phenyl derivatives. From these results, it can be concluded that the combining size of the agglutinin is as large as a disaccharide of the alpha-anomer of Gal at nonreducing end and most complementary to Galalpha1-->6Glc. As for the combining site of PA-IL toward the beta-anomer, the size is assumed to be less than that of Gal; carbon-6 in the pyranose form is essential, and hydrophobic interaction is important for binding.      

Patterns of Biofilm Succession on a Sheltered Rocky Shore in Hong Kong

Successional patterns are dependent on the nature of the substratum, water flow, concentrations of organics as well as the availability of bacteria, algal spores and invertebrate larvae in the coastal environment. Bacteria play an especially important role in biofilm formation as they are generally the earliest colonizers. In the present study, both winter and summer biofilm succession patterns were examined on glass coverslips inverted on experimental racks attached at two tidal levels on a sheltered shore in Hong Kong. In the succession, bacteria were followed by diatoms and cyanobacteria. Encrusting algae appeared in the late stages of the experiment (day 80 in summer and day 60 in winter). Colonization by bacteria was much slower in summer and their density remained low throughout the experimental period. The first appearance of diatoms and cyanobacteria, however, was more rapid in the summer. Bacteria and diatoms on the low-shore surfaces also had a faster succession rate than on the high-shore surfaces, suggesting that desiccation/aerial temperature are the causal factors for such differences.     

Potential of Selected Canadian Plant Species for Phytoextraction of Trace Elements From Selenium-Rich Soil Contaminated by Industrial Activity

In this preliminary screening study, we tested the phytoextraction potential of nine Canadian native/well-adapted plant species on a soil highly polluted by trace elements (TE) from a copper refinery. Plant physiological parameters and soil cover index were monitored for a 12-week period. At the end of the trial, biomass yield, bioconcentration (BFC) and translocation (TF) factors for the main TE as well as phytoextraction potential were determined. Most plants were severely injured by the high pollution levels, showing symptoms of toxicity including chlorosis, mortality and very low biomass yield. However, Indian mustard showed the highest selenium extraction potential (65 mg m^?2), even under harsh growing conditions. Based on our results, tall fescue and ryegrass, which mainly stored As, Cu, Pb and Zn within roots, could be used effectively for phytostabilization.     

Estimating root biomass in Salix viminalis × Salix schwerinii cultivar “Olof” using the electrical capacitance method

Abstract

Non‐destructive assessment of root systems is important in order to understand and optimise the potential of resource capture and allocation by the plant. We studied the relationships between electrical capacitance (EC) and the below‐ and above‐ground biomass of willows. Cuttings of Salix viminalis × Salix schwerinii cv. Olof were maintained in pots and root development was followed up using a portable capacitance meter over the course of 2.5 months. Pot observations were compared with excavation of two‐year‐old established trees. A strong significant linear relationship (R ² = 0.81, p < 0.001) was obtained between EC and root biomass (dry weight [DW]) for the pot experiment. EC also showed good correlations with stem and leaf biomass, as well as with stem height. In the excavated willow trees, there was a strong logarithmic relationship between EC and root biomass (R ² = 0.66, p < 0.001). These results suggest that EC is a good estimator of below‐ground biomass in willow and may become useful in screening varieties for differences in root biomass traits, especially in distinguishing below‐ground resource allocation at an early stage.     

Synemin promotes AKT-dependent glioblastoma cell proliferation by antagonizing PP2A

The intermediate filament protein synemin is present in astrocyte progenitors and glioblastoma cells but not in mature astrocytes. Here we demonstrate a role for synemin in enhancing glioblastoma cell proliferation and clonogenic survival, as synemin RNA interference decreased both behaviors by inducing G1 arrest along with Rb hypophosphorylation and increased protein levels of the G1/S inhibitors p21(Cip1) and p27(Kip1). Akt involvement was demonstrated by decreased phosphorylation of its substrate, p21(Cip1), and reduced Akt catalytic activity and phosphorylation at essential activation sites. Synemin silencing, however, did not affect the activities of PDPK1 and mTOR complex 2, which directly phosphorylate Akt activation sites, but instead enhanced the activity of the major regulator of Akt dephosphorylation, protein phosphatase type 2A (PP2A). This was accompanied by changes in PP2A subcellular distribution resulting in increased physical interactions between PP2A and Akt, as shown by proximity ligation assays (PLAs). PLAs and immunoprecipitation experiments further revealed that synemin and PP2A form a protein complex. In addition, treatment of synemin-silenced cells with the PP2A inhibitor cantharidic acid resulted in proliferation and pAkt and pRb levels similar to those of controls. Collectively these results indicate that synemin positively regulates glioblastoma cell proliferation by helping sequester PP2A away from Akt, thereby favoring Akt activation.     

Predation on eggs and larvae ofHeliothis virescens [Lep.: Noctuidae] by an adult predator complex in cage studies on cotton

Predation by a predator complex consisting of adults of the lygaeidGeocoris punctipes (Say), the nabidsNabis roseipennis Reuter and/orTropiconabis capsiformis Germar and the coccinelids,Hippodamia convergens Guerin-Meneville andColeomegilla maculata (DeGeer) onHeliothis virescens (F.) eggs, 1st-instar larvae or both on late pinhead square and early bloom stage cotton was evaluated in field cages in Mississippi. Prey densities of 4 (11, 512/ha) or 8 per cage and predator: prey (P:p) ratios of 1∶1, 2∶1, 3∶1, 4∶1 and 5∶1 were used. Prey were labeled with phosphorus-32 or carbon-14 to determine predator ingestion and effectiveness. Average percent egg predation as a function of P:p ratio ranged from 2.1 to 12.1 for a 48 h period. The average percent predation on larvae as a function of P:p ratio ranged from 5.3 to 22.0. The hemiptera fed more than the coleoptera on larvae, andG. punctipes was the best egg predator. For the range of predator densities used, the average area of discovery for the predator complex was 6.98 × 10⁻³ m/day and 2.34 × 10⁻² m/day when exposed to eggs and larvae, respectively. Publication N^o 5936-Mississippi Agricultural and Forestry Experiment Station, Mississippi State, MS 39762.     

Effect of self-association on the structural organization of partially folded proteins: inactivated actin

The propensity to associate or aggregate is one of the characteristic properties of many nonnative proteins. The aggregation of proteins is responsible for a number of human diseases and is a significant problem in biotechnology. Despite this, little is currently known about the effect of self-association on the structural properties and conformational stability of partially folded protein molecules. G-actin is shown to form equilibrium unfolding intermediate in the vicinity of 1.5 M guanidinium chloride (GdmCl). Refolding from the GdmCl unfolded state is terminated at the stage of formation of the same intermediate state. An analogous form, known as inactivated actin, can be obtained by heat treatment, or at moderate urea concentration, or by the release of Ca(2+). In all cases actin forms specific associates comprising partially folded protein molecules. The structural properties and conformational stability of inactivated actin were studied over a wide range of protein concentrations, and it was established that the process of self-association is rather specific. We have also shown that inactivated actin, being denatured, is characterized by a relatively rigid microenvironment of aromatic residues and exhibits a considerable limitation in the internal mobility of tryptophans. This means that specific self-association can play an important structure-forming role for the partially folded protein molecules.