Fine-Scale Dissection of Functional Protein Network Organization by Statistical Network Analysis

Revealing organizational principles of biological networks is an important goal of systems biology. In this study, we sought to analyze the dynamic organizational principles within the protein interaction network by studying the characteristics of individual neighborhoods of proteins within the network based on their gene expression as well as protein-protein interaction patterns. By clustering proteins into distinct groups based on their neighborhood gene expression characteristics, we identify several significant trends in the dynamic organization of the protein interaction network. We show that proteins with distinct neighborhood gene expression characteristics are positioned in specific localities in the protein interaction network thereby playing specific roles in the dynamic network connectivity. Remarkably, our analysis reveals a neighborhood characteristic that corresponds to the most centrally located group of proteins within the network. Further, we show that the connectivity pattern displayed by this group is consistent with the notion of “rich club connectivity” in complex networks. Importantly, our findings are largely reproducible in networks constructed using independent and different datasets.     

Chemical Composition and Pharmacological Evaluation and of Toddalia asiatica (Rutaceae) Extracts and Essential Oil by in Vitro and in Silico Approaches.

Toddalia asiatica (L.) Lam. is extensively used in traditional medicinal systems by various cultures. Despite its frequent use in traditional medicine, there is still a paucity of scientific information on T. asiatica growing on the tropical island of Mauritius. Therefore, the present study was designed to appraise the pharmacological and phytochemical profile of extracts (methanol, ethyl acetate and water) and essential oil obtained from aerial parts of T. asiatica. Biological investigation involved the evaluation of in vitro antioxidant and enzyme inhibitory potentials. The chemical profile of the EO was determined using gas chromatography coupled to mass spectrometry (GC/MS) analysis, while for the extracts, the total phenolic (TPC) and flavonoid content were quantified as well as their individual phenolic compounds by LC/MS/MS. Quinic acid, fumaric acid, chlorogenic acid, quercitrin and isoquercitrin were the main compounds in the extracts. Highest total phenolic (82.5±0.94 mg gallic acid equivalent (GAE/g)) and flavonoid (43.8±0.31 mg rutin equivalent (RE/g)) content were observed for the methanol extract. The GC/MS analysis has shown the presence of 26 compounds with linalool (30.9 %), linalyl acetate (20.9 %) and β-phellandrene (7.9 %) being most abundant components in the EO. The extracts and EO showed notable antioxidant properties, with the methanol extract proved to be superior source of antioxidant compounds. Noteworthy anti-acetylcholinesterase (AChE) and anti-butyrylcholinesterase (BChE) effects were recorded for the tested samples, while only the methanol and ethyl acetate extracts were active against tyrosinase. With respect to antidiabetic effects, the extracts and EO were potent inhibitors of α-glucosidase, while modest activity was recorded against α-amylase. Docking results showed that linalyl acetate has the highest affinity to interact with the active site of BChE with docking score of −6.25 kcal/mol. The findings amassed herein act as a stimulus for further investigations of this plant as a potential source of bioactive compounds which can be exploited as phyto-therapeutics.     

The Effect of Experimental Diabetes on the Twenty‐Four‐Hour Pattern of the Vasodilator Responses to Acetylcholine and Isoprenaline ın the Rat Aorta

The aim of this study was to investigate whether time‐dependent variations in the relaxant effect of acetylcholine, an endothelium‐dependent vasorelaxant via muscarinic receptors, and isoprenaline, a nonselective β‐adrenoceptor agonist in rat aorta, are influenced by streptozotocin (STZ)‐induced experimental diabetes. Adult male rats were divided randomly into two groups: control and STZ‐induced (STZ, 55 mg/kg, intraperitoneal) diabetes. The animals were synchronized to a 12∶12 h light‐dark cycle (lights on 08∶00 h) and sacrificed at six different times of day (1, 5, 9, 13, 17, and 21 hours after lights on; HALO) eight weeks after STZ injection. The in vitro responsiveness of thoracic aorta rings obtained from control and diabetic rats to acetylcholine (10^?9–10^?5 M) and isoprenaline (10^?10–10^?3 M) was determined in six different times. EC₅₀ (the concentration inducing half of the maximum response) values and maximum responses were calculated from cumulative concentration‐response curves of the agonists and were analyzed with respect to time and STZ treatment. Treatment, time, and interactions between treatment and time were tested by two‐way analysis of variance (ANOVA). To analyze differences due to biological time, one‐way ANOVA was used. STZ treatment did not significantly change EC₅₀ values or maximum responses for both agonists. There were statistically significant time‐dependent variations in the EC₅₀ values for isoprenaline and maximum responses for both acetylcholine and isoprenaline in control groups by one‐way ANOVA, but significant time‐dependent variations disappeared in the aortas isolated from STZ‐induced diabetic rats. The vasodilator responses to acetylcholine and isoprenaline failed to show any significant interaction (treatment×time of study) between STZ treatment and time of sacrifice in both EC₅₀ values and maximum responses by two‐way ANOVA. These results indicate there is a basic temporal pattern in the responses to acetylcholine and isoprenaline in rat aorta which continues in diabetes. It is shown for the first time that experimental diabetes does not change the 24 h pattern of responses to acetylcholine and isoprenaline, and that time‐dependent variations in the responses to these agonists disappear in diabetic animals. Although further studies are required to define the underlying mechanism(s) of these findings, results suggest that experimental diabetes can modify the time‐dependent vasorelaxant responses of rat aorta. This may help to understand the circadian rhythms in cardiovascular physiology and pathology or in drug effects in diabetes.     

Identification of extracellular enzyme producing alkalophilic bacilli from Izmir province by 16S-ITS rDNA RFLP

AIMS: To screen industrially important extracellular enzymes from the newly isolated alkalophilic bacilli and to characterize them by phenotypic and 16S-internal transcribed spacer (ITS) rDNA restriction pattern analysis. METHODS AND RESULTS: Three different environmental samples, soil, leather and horse faeces, were collected within the province of Izmir. Isolates grown on Horikoshi-I medium for 24 h at 37 degrees C were screened for extracellular enzyme activity by using eight different substrates: birchwood xylan, carboxymethylcellulose, casein, citrus pectin, polygalacturonic acid, soluble starch, and Tween 20 and 80. In total, 115 extracellular enzyme-producing bacilli were obtained. Casein was hydrolysed by 78%, soluble starch by 67%, citrus pectin by 63%, polygalacturonic acid by 62%, Tween 20 by 34%, birchwood xylan by 16%, Tween 80 by 12%, and carboxymethylcellulose by 3% of the isolates. The isolates were differentiated into 19 distinct homology groups by the 16S-ITS rDNA restriction pattern analysis. CONCLUSIONS: Eight different extracellular enzyme activities were determined in 115 endospore forming bacilli. The largest 16S-ITS rDNA homology group (HT1) included 36% of the isolates, 98% of which degraded casein, polygalacturonic acid, pectin and starch. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is the first report on the characterization of the industrial enzyme-producing alkalophilic bacilli by 16S-ITS rDNA restriction fragment length polymorphism (RFLP). Restriction profiles of 64% of the isolates were found to be different from those of five reference strains used.     

Receptor-mediated adenylyl cyclase activation through XLalpha(s), the extra-large variant of the stimulatory G protein alpha-subunit

XLalpha(s), the large variant of the stimulatory G protein alpha subunit (Gsalpha), is derived from GNAS1 through the use of an alternative first exon and promoter. Gs(alpha) and XLalpha(s) have distinct amino-terminal domains, but are identical over the carboxyl-terminal portion encoded by exons 2-13. XLalpha(s) can mimic some functions of Gs(alpha), including betagamma interaction and adenylyl cyclase stimulation. However, previous attempts to demonstrate coupling of XLalpha(s) to typically Gs-coupled receptors have not been successful. We now report the generation of murine cell lines that carry homozygous disruption of Gnas exon 2, and are therefore null for endogenous XLalpha(s) and Gs(alpha) (Gnas(E2-/E2-)). Gnas(E2-/E2-) cells transfected with plasmids encoding XLalpha(s) and different heptahelical receptors, including the beta2-adrenergic receptor and receptors for PTH, TSH, and CRF, showed agonist-mediated cAMP accumulation that was indistinguishable from that observed with cells transiently coexpressing Gs(alpha) and these receptors. Our findings thus indicate that XLalpha(s) is capable of functionally coupling to receptors that normally act via Gs(alpha).     

Evaluation of the immune response to hepatitis B vaccination in children aged 1-3 years in Malatya, Turkey

By the end of 1998, Turkey had launched the routine vaccination of infants against hepatitis B. The purpose of the study is to evaluate the immune response in a sample of vaccinated children aged 1-3 years in the city of Malatya. A total of 210 vaccinated children 12 to 48 months old were selected for the study with 30 cluster sampling in the city of Malatya, Turkey. The children were visited at their homes during January-April 2002. The information on demographic characteristics, family's and child's medical history was gathered, childrens' weight and height were measured and blood samples were taken. Anti-HBs, HbsAg and anti-HBc titers were assayed by micro-ELIZA from the sera. The mean age of the children was 26.3 months, 100 (47.6%) were male and 110 (52.4%) were female. Overall, 203 (96.7%) children had protective anti-HBs levels (> or = 10 IU/l), 0.5% showed evidence of natural infection (with positive anti-HBc and anti-HBs titers), 0.5% had acute or chronic infection (with positive HbsAg and anti-HBc titers) and 2.3% were seronegative. Geometric mean titer of anti-HBs among vaccinated children except those who had positive anti-HBc titers was 138.7 mIU/ml (95% CI:124.7-154.2) and seroconversion rates did not differ by age, sex, anthropometric measurements, time after third dose and place of vaccine administered (P > 0.05). The high seroprotection rate over 95% showed that routine infant vaccination program for hepatitis B was successfully carried out in the city Malatya.     

Cocultivation of Lactococcus lactis and Teredinobacter turnirae for biological chitin extraction from prawn waste

In this study, mainly biological treatment of prawn waste for chitin production was investigated. Lactic acid and protease fermentations were applied to extract chitin from prawn waste in the presence of various glucose concentrations. The results obtained were also compared with those of chemical method which was consisted of first mineral removal and then protein removal sequence. Different strategies were applied using lactic acid producing bacterium, Lactococcus lactis, and a protease producer, marine bacterium Teredinobacter turnirae. Both bacteria were first cultivated individually and then cofermented. In their individual cultivation, L. lactis removed the inorganic materials efficiently, while T. turnirae performed better in deproteinization process. Cofermentation of both bacteria was also conducted using three different protocols. The highest process yield (95.5%) was obtained when T. turnirae was first inoculated. Although the extraction of chitin by biological treatment was incomplete compared to the chemical method, the biological treatment employed here could still be considered as an alternative method in a more environmentally benign approach.     

Simple sequence repeat-based assessment of genetic relationships among Prunus rootstocks

Ten SSR loci, previously developed for Prunus, were analyzed to examine genetic relationships among 23 rootstock candidates for sweet and sour cherries, of the species P. avium, P. cerasus, P. mahaleb, and P. angustifolia. Five genotypes of P. laurocerasus, not used as rootstock, were included in the molecular analysis. The number of alleles per locus ranged from 8 to 12, with a mean of 9, while the number of microsatellite genotypes varied from 8 to 17, indicating that the SSRs were highly informative. The degree of heterozygosity (0.61) was high. Clustering analysis resulted in two main clusters. The first cluster was divided into two subclusters; the first subcluster consisted of P. avium and P. cerasus, and the second subcluster consisted of P. laurocerasus. The second cluster was divided into two subclusters. The first subcluster consisted of P. mahaleb genotypes and the second consisted of P. angustifolia genotypes. The reference rootstocks also clustered with their associated botanical species. Unweighted pair-group method with arithmetic mean analysis demonstrated that P. laurocerasus genotypes had less genetic variation and that P. avium genotypes were more closely related to P. cerasus. The SSR-based phylogeny was generally consistent with Prunus taxonomy information, suggesting the applicability of SSR analysis for genotyping and phylogenetic studies in the genus Prunus.