Using pathway modules as targets for assay development in xenobiotic screening

Toxicology and pharmaceutical research is increasingly making use of high throughout-screening (HTS) methods to assess the effects of chemicals on molecular pathways, cells and tissues. Whole-genome microarray analysis provides broad information on the response of biological systems to chemical exposure, but is not practical to use when thousands of chemicals need to be evaluated at multiple doses and time points, as well as across different tissues, species and life-stages. A useful alternative approach is to identify a focused set of genes that can give a coarse picture of systems-level responses and that can be scaled to the evaluation of thousands of chemicals and diverse biological contexts. We demonstrate a computational approach to select in vitro expression assay targets that are informative and broadly distributed in biological pathway space, using the concept of pathway modularity. Canonical pathways are decomposed into subnetworks (modules) of functionally-related genes based on rules such as co-regulated expression, protein-protein interactions, and coordinated physiological activity. Pathway modules are constructed using these rules but are then restricted by the bounds of canonical pathways. We demonstrate this approach using a subset of genes associated with tumor development and cancer progression. Target genes were identified for assay development, and then validated by using independent, published microarray data. The result is a targeted set of genes that are sensitive predictors of whether a chemical will perturb each pathway module. These selected genes could then form the basis for a battery to test for pathway-chemical interactions under many biological contexts using throughput expression-based assays.     

Warthin''s tumour: unusual vs. common morphological findings in fine needle aspiration biopsies

Fine needle aspiration biopsies (FNA) of 47 Warthin's tumours confirmed by histology were re-evaluated for cytomorphological findings. The majority of aspirates (37/47) contained a typical background with proteinaceous substance and cell debris, along with cellular elements represented by oncocytic, lymphoid, and mast cells with degranulated cytoplasm. Uncommon cellular findings were true squamous cells (1/47), atypical cells with vacuoles (1/47), osteoclastic giant cells (1/47), epithelioid cells (1/47), mast cells with preserved granules in cytoplasm (3/47), and siderophages (4/47). Uncommon findings in the background were corpora amylacea-like structures and homogeneous bright red droplets. Squamous cells and atypical cells with vacuoles caused diagnostic difficulties in distinguishing a Warthin's tumour from a squamous cell or mucoepidermoid carcinoma. However, other unusual cellular and background findings were not worrying; therefore, they are merely regarded as a curiosity in the cytomorphological appearance of the tumour.     

Performance of Cryptolaemus montrouzieri feeding on Pulvinaria aurantii ovisacs on citrus plants

We studied the performance of the coccinellid Cryptolaemus montrouzieri on citrus plant species infested with orange pulvinaria scale, Pulvinaria aurantii, under controlled conditions in the laboratory. The experimental host plants were blood orange, grapefruit, lemon, pummelo and kumquat. All life history parameters indicated best performance of C. montrouzieri, when reared on P. aurantii ovisacs on the leaves of grapefruit. Pummelo, blood orange, lemon or kumquat were less suitable.     

North African wetland lakes: characterization of nine sites included in the CASSARINA Project

Exploitation of land and water resources has increased rapidly in North Africa during the 20th century, paralleling regional population growth. As part of the CASSARINA Project (see Flower, 2001), the environmental status of nine wetland lakes in Morocco, Tunisia, and Egypt was evaluated. All are conservationally important habitats and several are Ramsar Sites (internationally recognized bird reserves) and several support significant fisheries. All are shallow (<2 m in depth) but vary greatly in area.Where available, documentary information on relevant 20th century changes is given. Survey transects for aquatic vegetation were established and used to provide baseline ecological information on the aquatic plant communities during 1997–1999. Unusually, one site (Tunisian Megene Chitane) supported acidophilous vegetation (some taxa being nationally rare). Aquatic macrophytes declined catastrophically at two sites during the 1990s. Merja Bokka was drained in 1998 and, at Garaet El Ichkeul, fringing Phragmites and Scirpus spp. were lost, mainly as a result of salinity changes. Elsewhere, fringing macrophytes remain (extensively so in the Nile Delta lakes) common, despite major land reclamation and water quality problems, or are degraded by grazing (Merja Zerga). Marginal vegetation during 1997/98 changed markedly at Megene Chitane due to water level lowering.Documentary records indicated that throughout the 20th century, reclamation and hydrologic modifications, mainly for agricultural purposes, affected all nine sites. The loss of lake area by reclamation is substantial for the Nile Delta lakes (Edku, Burullus and Manzala). For the western sites, some data indicate increasing salinity in the most recent decade but the Delta lakes have become generally fresher during the 20th century, as supply of Nile water for irrigation increased.Despite intense human disturbance, many of the remaining CASSARINA sites still support regions of high aquatic diversity. Spatial scale monitoring of the larger sites for seasonal and inter-annual changes in open water area and in aquatic plant abundances is a key requirement for integrated environmental change assessment in the 21st century.     

Antibacterial activity of selected medicinal plants of northwest Pakistan traditionally used against mastitis in livestock

The present study aimed to investigate the efficacy of traditionally used anti-mastitis plants (Allium sativum, Bunium persicum, Oryza sativa and Triticum aestivum) in northwest Pakistan against bacterial pathogens. Selected plants were phytochemically screened for Alkaloids, Flavonoids, and Saponins and checked for in vitro antibacterial activity at concentration of 50 mg/ml against S. aureus, E. coli and K. pneumoniae by agar well diffusion method. Minimum inhibitory concentration and minimum bactericidal concentration was determined against multidrug resistant bacteria using tube dilution method. All extracts were found to significantly inhibit (p < 0.01, p < 0.05) the activity against bacterial strains examined. Among phytochemicals, alkaloids of all tested antimastitis plants produced significantly higher inhibition zones against bacteria. The minimum inhibitory concentration and minimum bactericidal concentration of phytochemicals and crude methanolic extracts against tested bacterial strains ranged between 12.5–50 mg/ml and 25–50 mg/ml, respectively. Medicinal plants traditionally used against mastitis are therapeutically active against bacterial pathogens. A. sativum and B. persicum were found to be potential candidate species for the development of novel veterinary drugs with low cost and fewer side effects.     

Effects of carbon dioxide exposure on early brain development in rats

The developing brain is vulnerable to environmental factors. We investigated the effects of air that contained 0.05, 0.1 and 0.3% CO₂ on the hippocampus, prefrontal cortex (PFC) and amygdala. We focused on the circuitry involved in the neurobiology of anxiety, spatial learning, memory, and on insulin-like growth factor-1 (IGF-1), which is known to play a role in early brain development in rats. Spatial learning and memory were impaired by exposure to 0.3% CO₂ air, while exposure to 0.1 and 0.3% CO₂ air elevated blood corticosterone levels, intensified anxiety behavior, increased superoxide dismutase (SOD) enzyme activity and MDA levels in hippocampus and PFC; glutathione peroxidase (GPx) enzyme activity decreased in the PFC with no associated change in the hippocampus. IGF-1 levels were decreased in the blood, PFC and hippocampus by exposure to both 0.1 and 0.3% CO₂. In addition, apoptosis was increased, while cell numbers were decreased in the CA1 regions of hippocampus and PFC after 0.3% CO₂ air exposure in adolescent rats. A positive correlation was found between the blood IGF-1 level and apoptosis in the PFC. We found that chronic exposure to 0.3% CO₂ air decreased IGF-1 levels in the serum, hippocampus and PFC, and increased oxidative stress. These findings were associated with increased anxiety behavior, and impaired memory and learning.     

Bayesian and Phylogenic Approaches for Studying Relationships among Table Olive Cultivars

To enhance table olive tree authentication, relationship, and productivity, we consider the analysis of 18 worldwide table olive cultivars (Olea europaea L.) based on morphological, biological, and physicochemical markers analyzed by bioinformatic and biostatistic tools. Accordingly, we assess the relationships between the studied varieties, on the one hand, and the potential productivity–quantitative parameter links on the other hand. The bioinformatic analysis based on the graphical representation of the matrix of Euclidean distances, the principal components analysis, unweighted pair group method with arithmetic mean, and principal coordinate analysis (PCoA) revealed three major clusters which were not correlated with the geographic origin. The statistical analysis based on Kendall’s and Spearman correlation coefficients suggests two highly significant associations with both fruit color and pollinization and the productivity character. These results are confirmed by the multiple linear regression prediction models. In fact, based on the coefficient of determination (R ²) value, the best model demonstrated the power of the pollinization on the tree productivity (R ² = 0.846). Moreover, the derived directed acyclic graph showed that only two direct influences are detected: effect of tolerance on fruit and stone symmetry on side and effect of tolerance on stone form and oil content on the other side. This work provides better understanding of the diversity available in worldwide table olive cultivars and supplies an important contribution for olive breeding and authenticity.