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1.
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. 相似文献
2.
Devina Lobine Bryan Pairyanen Gokhan Zengin Mustafa Abdullah Yılmaz Rayene Ouelbani Souheir Bensari Gunes Ak Hassan H. Abdallah Muhammad Imran Mohamad Fawzi Mahomoodally 《化学与生物多样性》2021,18(4):e2000999
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. 相似文献
3.
Bastepe M Gunes Y Perez-Villamil B Hunzelman J Weinstein LS Jüppner H 《Molecular endocrinology (Baltimore, Md.)》2002,16(8):1912-1919
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). 相似文献
4.
Karaoglu L Pehlivan E Gunes G Genc M Tekerekoglu SM Ercan C Egri M Yologlu S 《The new microbiologica》2003,26(4):311-319
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. 相似文献
5.
Akbalik G Gunes H Yavuz E Yasa I Harsa S Elmaci ZS Yenidunya AF 《Journal of applied microbiology》2004,97(4):766-773
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. 相似文献
6.
Interactive effects of boron and salinity stress on the growth,membrane permeability and mineral composition of tomato and cucumber plants 总被引:8,自引:1,他引:8
A greenhouse study was conducted in order to determine interactive effects of NaCl salinity and B on the growth, sodium (Na), chloride (Cl), boron (B), potassium (K) concentrations and membrane permeability of salt resistant Tomato (Lycopersicon esculentum L. cv. Lale F1) and salt sensitive cucumber (Cucumis sativus L. cv. Santana F1) plants. Plants were grown in a factorial combination of NaCl (0 and 30 mM for cucumber and 0 and 40 mM for tomato) and B (0, 5, 10 and 20 mg kg–1 soil). Boron toxicity symptoms appeared at 5 mg kg–1 B treatments in both plants. Salinity caused an increase in leaf injury due to B toxicity, but it was more severe in cucumber. Dry weights of the plants decreased with the increasing levels of applied B in nonsaline conditions, but the decrease in dry weights due to B toxicity was more pronounced in saline conditions especially in cucumber. Salinity × B interaction on the concentration of B in both plants was found significant. However, increase in B concentrations of tomato decreased under saline conditions when compared to nonsaline conditions. Contrary to this, B concentration of cucumber increased as a result of increasing levels of applied B and salinity. Salinity increased Na and Cl concentrations of both plants.Potassium concentration of tomato was not affected by salinity and B treatments, but K concentration of cucumber was decreased by salinity. Membrane permeability of the plants was increased by salinity while toxic levels of B had no effect on membrane permeability in nonsaline conditions. Membrane permeability was significantly increased in the presence of salinity by the increasing levels of applied B. 相似文献
7.
Gokhan Bayramoglu Hulyam Kurt Aysegul Bayramoglu Hasan Veysi Gunes İrfan Degirmenci Suat Colak 《Cytotechnology》2015,67(5):845-849
There is little information about the hepatoprotective effects of gallic acid against ischemia–reperfusion (I/R) damage. Animals were subjected to I/R. Gallic acid at doses of 50 and 100 mg/kg body weight (bw) were injected as a single dose prior to ischemia. Liver tissue homogenates were used for the measurement of malondialdehyde (MDA), catalase (CAT) and glutathione peroxidase (GPx) levels. At the same time alanine aminotransferase (ALT), aspartate aminotransferase (AST) and lactate dehydrogenase (LDH) were assayed in serum samples and compared statistically. While the ALT, AST, LDH activities and MDA levels were significantly increased, CAT and GPx activities significantly decreased in only I/R-induced control rats compared to normal control rats (P < 0.05). Treatment with gallic acid at a dose of 100 mg/kg bw significantly decreased the ALT, AST, LDH activities and MDA levels, and markedly increased activities of CAT and GPx in tissue homogenates compared to I/R-induced rats with no treatment group (P < 0.05). In oxidative stress generated by hepatic ischemia–reperfusion, gallic acid contributes partially an alteration in the delicate balance between the scavenging capacity of antioxidant defense systems and free radicals in favour of the antioxidant defense systems in the body. 相似文献
8.
Turkoglu Z Bilgener S Ercisli S Bakir M Koc A Akbulut M Gercekcioglu R Gunes M Esitken A 《Genetics and molecular research : GMR》2010,9(4):2156-2165
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. 相似文献
9.
Gunes A Inal A Alpaslan M Eraslan F Bagci EG Cicek N 《Journal of plant physiology》2007,164(6):728-736
It has been proposed that salicylic acid (SA) acts as an endogenous signal molecule responsible for inducing abiotic stress tolerance in plants. The effect of varying salicylic acid (SA) supply (0, 0.1, 0.5 and 1.0mM) on growth, mineral uptake, membrane permeability, lipid peroxidation, H(2)O(2) concentration, UV-absorbing substances, chlorophyll and carotenoid concentrations of NaCl (40 mM) stressed maize (Zea mays L.) was investigated. Exogenously applied SA increased plant growth significantly both in saline and non-saline conditions. As a consequence of salinity stress, lipid peroxidation, measured in terms of malondialdehyde (MDA) content and membrane permeability was decreased by SA. UV-absorbing substances (UVAS) and H(2)O(2) concentration were increased by increasing levels of SA. SA also strongly inhibited Na(+) and Cl(-) accumulation, but stimulated N, Mg, Fe, Mn and Cu concentrations of salt stressed maize plants. These results suggest that SA could be used as a potential growth regulator to improve plant salinity stress resistance. 相似文献
10.
The effect of silicon (Si) on the growth, sodium (Na), chloride (Cl), boron (B) concentrations, lipid peroxidation (MDA), membrane permeability (MP), lypoxygenase activity (LOX), proline (PRO) and H(2)O(2) accumulation, and the activities of major antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT and ascorbate peroxidase, APX) of barley grown in original sodic-B toxic soil were investigated. Si applied to the sodic-B toxic soil at 70, 140 and 280 mg kg(-1) levels significantly increased Si concentrations of the plants and counteracted the deleterious effects of sodicity (Na ions) and B on shoot growth. Membrane permeability and the concentrations of H(2)O(2) and MDA increased, while PRO concentration decreased in plants grown in sodic-B toxic soil without Si. LOX activity was increased by applied Si. Compared with control plants, the activities of SOD and CAT were decreased, but APX was increased by applied Si levels. 相似文献