Use of real-time PCR to discriminate parasitic and saprophagous behaviour by nematophagous fungi

Entomopathogenic nematodes (EPNs) are important pathogens of soilborne insects and are sometimes developed commercially to manage insect pests. Numerous nematophagous fungal species (NF) prey on nematodes and are thought to be important in regulating natural or introduced EPN populations. However, nematophagy by these fungi in nature cannot be inferred using existing methods to estimate their abundance in soil because many of these fungi are saprophytes, resorting to parasitism primarily when certain nutrients are limiting. Therefore, we developed an assay to quantify NF DNA in samples of nematodes. Species-specific primers and TaqMan probes were designed from the ITS rDNA regions of Arthrobotrys dactyloides, Arthrobotrys oligospora, Arthrobotrys musiformis, Gamsylella gephyropagum and Catenaria sp. When tested against 23 non-target fungi, the TaqMan real-time PCR assay provided sensitive and target-specific quantification over a linear range. The amount of A. dactyloides or Catenaria sp. DNA in 20 infected nematodes, measured by real-time PCR, differed between fungal species (P=0.001), but not between experiments (P>0.05). However, estimates of relative NF parasitism using a bioassay with 20 nematodes infected by either species, differed greatly (P<0.001) depending on whether the fungi were alone or combined in the samples used in the assay. Tests done to simulate detection of NF DNA in environmental samples showed that, for all species, background genomic DNA and/or soil contaminants reduced the quantity of DNA detected. Nested PCR was ineffective for increasing the detection of NF in environmental samples. Indeed, real-time PCR detected higher amounts of NF DNA than did nested PCR. The spatial patterns of NF parasitism in a citrus orchard were derived using real-time PCR and samples of nematodes extracted from soil. The parasitism by Catenaria sp. was positively related to the abundance of both heterorhabditid and steinernematid EPNs. The possible significance of the associations is ambiguous because NF attack a broad range of nematode taxa whereas EPNs are a small minority of the total nematode population in a soil sample. These studies demonstrate the potential of real-time PCR to study the role of NF parasitism in soil food webs.     

Entomopathogenic nematodes, root weevil larvae, and dynamic interactions among soil texture, plant growth, herbivory, and predation

Greenhouse experiments were conducted to assess the influence of soil texture on the persistence, efficacy and plant protection ability of entomopathogenic nematodes (EPNs) applied to control larvae of the Diaprepes root weevil (DRW), Diaprepes abbreviatus, infesting potted citrus seedlings. Seedlings were grown in pots containing either coarse sand, fine sand, or sandy loam. Three DRW larvae were added to each of 80 pots of each soil type. 24 h later, 20 pots of each soil type that had received weevil larvae were inoculated with EPN infective juveniles (IJs) of one of the following species: Steinernema diaprepesi, Steinernema riobrave and Heterorhabditis indica. Pots of each soil without EPNs were established as controls with DRW and controls without DRWs. Subsequently, pots with larvae received three additional larvae monthly, and the experiment continued for 9 months. Plant root and top weights at the end of the experiment were affected by both soil (P≤0.0001) and nematodes (P≤0.0001), and nematode species protected plants differently in different soils (interaction P≤0.0001). Soil porosity was inversely related to plant damage by DRW, whether or not EPNs were present; and porosity was directly related to the level of plant protection by EPNs. Mortality of caged sentinel weevil larvae placed in pots near the end of the experiment was highest in pots treated with S. diaprepesi. In a second, similar experiment that included an additional undescribed steinernematid of the Steinernema glaseri-group, soil type affected root damage by DRW and root protection by EPNs in the same manner as in the first experiment. Final numbers of S. diaprepesi and Steinernema sp. as measured by real-time PCR were much greater than those of S. riobrave or H. indica in all soils. Across all treatments, the number of weevil larvae in soil at the end the experiment was inversely related to soil porosity. In all soils, fewer weevil larvae survived in soil treated with S. diaprepesi or Steinernema sp. than in controls with DRW or treatments with S. riobrave or H. indica. The results of these experiments support the hypothesis that EPNs provide greater protection of seedlings against DRW larvae in coarse textured soil than in finer textured soil. However, less vigorous growth of the control without DRW seedlings in the two finer textured soils suggests that unidentified factors that stressed seedlings in those soils also impaired the ability of seedlings to tolerate weevil herbivory.     

Establishment of the enzymatic protein acetylation independent of acetyl CoA: recombinant glutathione S-transferase 3-3 is acetylated by a novel membrane-bound transacetylase using 7,8-diacetoxy-4-methyl coumarin as the acetyl donor

The current knowledge on biological protein acetylation is confined to acetyl CoA-dependent acetylation of protein catalyzed by specific acetyl transferases and the non-enzymatic acetylation of protein by acetylated xenobiotics such as aspirin. We have discovered a membrane-bound enzyme catalyzing the transfer of acetyl groups from the acetyl donor 7,8-diacetoxy-4-methyl coumarin (DAMC) to glutathione S-transferase 3-3 (GST3-3), termed DAMC:protein transacetylase (TAase). The purified enzyme was incubated with recombinant GST3-3 subunit and DAMC, the modified protein was isolated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) in gel digested with trypsin and the tryptic digest was analyzed by mass spectrometry. The N-terminus and six lysines, Lys-51, -82, -124, -181, -191 and -210, were found to be acetylated. The acetylation of GST3-3 described above was not observed in the absence of either DAMC or TAase. These results clearly establish the phenomenon of protein acetylation independent of acetyl CoA catalyzed by a hitherto unknown enzyme (TAase) utilizing a certain xenobiotic acetate (DAMC) as the active acetyl donor.     

Analysis of P-Loop and its Flanking Region Subsequence of Diverse NTPases Reveals Evolutionary Selected Residues

The P-loop NTPases are involved in diverse cellular functions. Members of the P-loop NTPase superfamily are characterized by presence of a highly conserved sequence pattern GxxxxGKS/T, known as Walker A motif. This motif adopts an archetypal P-loop conformation which allows accommodation of the triphosphate moiety of a bound nucleotide. Despite the presence of Walker A as a common sequence motif, P-loop NTPases exhibit extreme sequence divergence which hampers their phylogenetic or evolutionary classification. Here, we show that P-loop and its flanking region subsequence (termed as “extended-WalkerA motif”) contain distinct signatures that can be utilized to classify NTPase domain of functionally diverse proteins. We find a clearly classified group of diverse NTPases of Conserved Domain Database such as G-proteins, Ylqf, RecA like, DExDc, AAA, CPT, NK, ABC transporter and NifH proteins.     

Improved catalytic efficiency of a monomeric γ-glutamyl transpeptidase from Bacillus licheniformis in presence of subtilisin

Monomeric 30 kDa γ-glutamyl transpeptidase (GGT₃₀) was purified from culture broth of Bacillus licheniformis ER-15 along with a heterodimeric 67 kDa GGT (GGT₆₇). In presence of subtilisin, GGT₃₀ had improved catalytic efficiency (V_max/K_m) of 59 min^?1, altered pH and temperature optima of pH 11 and 70°C.and had salt-tolerant glutaminase activity. Glutaminase activity was retained even in protease-inhibited condition in presence of 2 mM PMSF. GGT₃₀ and subtilisin complexation was also confirmed by relative electrophoretic mobility and fluorescence quenching experiment.     

The FLIGHT Drosophila RNAi database: 2010 update

FLIGHT (http://flight.icr.ac.uk/) is an online resource compiling data from high-throughput Drosophila in vivo and in vitro RNAi screens. FLIGHT includes details of RNAi reagents and their predicted off-target effects, alongside RNAi screen hits, scores and phenotypes, including images from high-content screens. The latest release of FLIGHT is designed to enable users to upload, analyze, integrate and share their own RNAi screens. Users can perform multiple normalizations, view quality control plots, detect and assign screen hits and compare hits from multiple screens using a variety of methods including hierarchical clustering. FLIGHT integrates RNAi screen data with microarray gene expression as well as genomic annotations and genetic/physical interaction datasets to provide a single interface for RNAi screen analysis and datamining in Drosophila.Key words: RNAi, database, integration, bioinformatics, phenotype     

The changing epidemiology of dengue in Delhi, India

The distribution of deformed wing virus infection within the honey bee reproductive castes (queens, drones) was investigated by in situ hybridization and immunohistology from paraffin embedded sections. Digoxygenin or CY5.5 fluorochrome end-labelled nucleotide probes hybridizing to the 3' portion of the DWV genome were used to identify DWV RNA, while a monospecific antibody to the DWV-VP1 structural protein was used to identify viral proteins and particles. The histological data were confirmed by quantitative RT-PCR of dissected organs. Results showed that DWV infection is not restricted to the digestive tract of the bee but spread in the whole body, including queen ovaries, queen fat body and drone seminal vesicles.     

Role of highly central residues of P-loop and it's flanking region in preserving the archetypal conformation of Walker A motif of diverse P-loop NTPases

P-loop NTPases represent a large and highly diverse protein family that is involved in variety of cellular functions. Walker A motif forms a typical arched conformation, necessary to accommodate the phosphate moiety of the nucleoside tri (or di-) phosphate in Ploop NTPases. The feature that maintains the ancient architecture of P-loop is unidentified and uncharacterized. Here, using a well established global network parameter, closeness centrality, we identify that Walker A and its flanking regions (N- and C-terminal) have high density of globally connected residue positions. We find that closeness centrality of these residue positions are conserved across common structural core of diverse domains of P-loop NTPase fold. Our results suggest the potential role of globally connected residues in maintaining the local conformation of P-loop.