The role of circulating tumor cells and K-ras mutations in patients with locally advanced rectal cancer: a prospective study

Molecular Biology Reports - Rectal cancer is a common malignancy with a relatively poor prognosis. We assessed the possible prognostic and predictive role(s) of circulating tumor cells (CTCs) and...     

Isolation of new cytotoxic metabolites from Cleome droserifolia growing in Egypt

The sulforhodamine B (SRB) assay was used to assess the cytotoxicity of the aqueous (AqEx) and ethanolic (AlEx) extracts, respectively, of the aerial parts of Cleome droserifolia (Forssk.) Del. against two human cancer cell lines, breast (MCF7) and colon (HCT116) adenocarcinoma. AqEx exhibited higher cytotoxic activity, thus its four subfractions, namely n-hexane (HxFr), chloroform (ClFr), ethyl acetate (EtFr), and n-butanol (BuFr) fractions, were also tested. Purification of the more active ClFr and EtFr yielded nine compounds. Six terpenoids, guai-7(11),8-diene (C1), 1-hydroxy-guai-3,10(14)-diene (C2), 18-hydroxydollabela-8(17)-ene (C3), (24E)-stigmasta-5,8-dien-3beta-ol (C4), teucladiol [1alpha,5beta-guai-10(14)-ene-4beta,6beta-diol] (C5), and buchariol (4,10-epoxy-6a-hydroxyguaiane) (C6), were isolated from ClFr and three flavonol glycosides, isorhamnetin-3-O-beta-D-glucoside (F1), quercetin-3'-methoxy-3-O-(4"-acetylrhamnoside)-7-O-alpha-rhamnoside (F2), and kaempferol-4'-methoxy-3,7-O-dirhamnoside (F3), were isolated from EtFr. Compounds C3 and F2 are new in nature. The isolated compounds were identified using various spectroscopic methods (UV, IR, 1H NMR, 13C NMR, HMQC, HMBC, and COSY). Compounds C1, C3, F2, and F3 showed significant cytotoxic activities against the two tested cell lines comparable to those of the anticancer drug doxorubicin. The new compound C3 was the most active as it had the lowest IC50 values, (1.9 +/- 0.08) and (1.6 +/- 0.09) microg/ml corresponding to 6.5 and 5.4 microM, against MCF7 and HCT116 cells, respectively.     

Drug-target interaction prediction via class imbalance-aware ensemble learning

Background

Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train classifiers with the purpose of predicting new undiscovered interactions. However, a key challenge regarding this data that has not yet been addressed by these methods, namely class imbalance, is potentially degrading the prediction performance. Class imbalance can be divided into two sub-problems. Firstly, the number of known interacting drug-target pairs is much smaller than that of non-interacting drug-target pairs. This imbalance ratio between interacting and non-interacting drug-target pairs is referred to as the between-class imbalance. Between-class imbalance degrades prediction performance due to the bias in prediction results towards the majority class (i.e. the non-interacting pairs), leading to more prediction errors in the minority class (i.e. the interacting pairs). Secondly, there are multiple types of drug-target interactions in the data with some types having relatively fewer members (or are less represented) than others. This variation in representation of the different interaction types leads to another kind of imbalance referred to as the within-class imbalance. In within-class imbalance, prediction results are biased towards the better represented interaction types, leading to more prediction errors in the less represented interaction types.

Results

We propose an ensemble learning method that incorporates techniques to address the issues of between-class imbalance and within-class imbalance. Experiments show that the proposed method improves results over 4 state-of-the-art methods. In addition, we simulated cases for new drugs and targets to see how our method would perform in predicting their interactions. New drugs and targets are those for which no prior interactions are known. Our method displayed satisfactory prediction performance and was able to predict many of the interactions successfully.

Conclusions

Our proposed method has improved the prediction performance over the existing work, thus proving the importance of addressing problems pertaining to class imbalance in the data.

     

Assessment of titanium dioxide nanoparticles toxicity via oral exposure in mice: effect of dose and particle size

Objective: The aim of the present work is to evaluate the toxicity of titanium dioxide nanoparticles (TiO₂NPs) according to their doses and particle sizes.

Materials and methods: The effect of five days oral administration of TiO₂NPs (21 and 80?nm) with different doses (50, 250 and 500?mg/kg body weight) was assessed in mice via measurement of oxidative stress markers; glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), malondialdehyde (MDA) and nitric oxide (NO), liver function indices; aspartate and alanine aminotransferases (AST and ALT), chromosomal aberrations and liver histopathological pattern.

Results: The results revealed drastic alterations in all the measured parameters and showed positive correlation with the gradual dose increment. In addition, the smaller particle size of TiO₂NPS (21?nm) had more adverse effect in all the selected biochemical parameters, genetic aberrations and histological investigations.

Conclusions: Toxicity of TiO₂NPs increases in a dose-dependent manner and vice versa with particles size. The evaluated biomarkers are good indicators for TiO₂NPs toxicity. More detailed studies are required before the recommendation of TiO₂NP_S as food additives.     

Interactions between Glutathione-S-Transferase M1, T1 and P1 polymorphisms and smoking,and increased susceptibility to esophageal squamous cell carcinoma

Background: A complex of genetic and environmental factors is involved in carcinogenesis of the esophageal squamous cell carcinoma (ESCC). Glutathione-S-Transferases (GSTs) are phase-II enzymes playing role in detoxification of carcinogen electrophiles. Genetic polymorphisms of GSTM1, GSTT1 and GSTP1 in association with some environmental factors and their impact on esophageal cancer susceptibility were assessed in the Iranian population. Methods: Genomic DNA of peripheral blood leukocytes from 148 confirmed esophageal cancer cases and 137 healthy individuals as control group was assayed for restriction fragment length polymorphisms in the GSTP1 loci by PCR amplification followed by digestion with Alw26I. Deletion of the GSTM1 and GSTT1 genes was detected by multiplex PCR. A data-mining method based on decision trees was applied to produce a predictive model of interactions between genotypes. Results: Smoking was independently associated with ESCC (p < 0.05, OR: 2.286, 95% CI = 1.311–3.983). Smoking along with GSTP1 Val/Val genotype was associated to ESCC (p < 0.001, OR: 3.886, 95% CI = 1.830–8.251), while non-smokers with GSTP1 Val/Val were significantly more frequent in non-cancerous group. (p = 0.007, OR: 0.507, 95% CI = 0.309–0.830). Conclusions: Data-mining methods are useful tools to map out a scheme for predicting complex relations and combinations of different genotypes. Genotyping analysis of GSTP1 together with assessment of smoking seems to be important in determining the risk of ESCC in the Iranian population.     

Materials forPythium flora of Japan. X. Occurrence,identification and seasonality ofPythium spp. in three pond waters and mud soils in Osaka

Seasonal fluctuations ofPythium species in three pond waters and mud soils in Sakai, Osaka, were studied for periods of two years and 14 months, respectively. Thirteen species and four groups were isolated from the pond waters while nine species and three groups were obtained from the mud soils. The highest frequency and total number of species were recorded in the cold and moderately warm seasons and the lowest in summer. Most of the species isolated from the pond waters have been previously recorded from aquatic habitats.     

Biotic and abiotic initiators for rishitin formation and accumulation in tomato

γ-Ray irradiation of pre-sowing seeds of tomato did not trigger the formation of the phytoalexin “rishitin” in either leaves or fruits of tomato plants through different growth seasons. Application of copper sulfate initiated rishitin formation in both leaves and fruits. Increasing of γ-ray dose was accompanied by decreasing rishitin accumulation in the presence of copper sulfate. Rishitin of tomato leaves was found to be reduced significantly, concomitant with increasing the disease incidence for late and early blight, andFusarium wilt disease, after applying γ-irradiation, in the case of biotic initiatorsPhytophthora infestans, Alternaria solani orFusarium oxysporum alone or together with the abiotic inducer copper sulfate. Shelf-extending γ-ray doses of 1.0, 1.5 and 2.0 kGy decreased rishitin amounts in tomato fruits treated with copper sulfate alone or infected withPhytophthora infestans. Also, the amount of formed rishitin was reduced by extending the storage period.     

Molecular Mapping and Characterization of Genes Governing Time to Flowering, Seed Weight, and Plant Height in an Intraspecific Genetic Linkage Map of Chickpea (Cicer arietinum)

Drought is the major constraint to chickpea productivity worldwide. Utilizing early flowering genotypes and larger seed size have been suggested as strategies for breeding in drought zones. Therefore, this study aimed to identify potential markers linked to days-to-flowering, 100-seed weight, and plant height in a chickpea intraspecific F_2:3 population derived from the cross ILC3279 × ICCV2. A closely linked marker (TA117) on linkage group LG3 was identified for the days-to-flowering trait, explaining 33% of the variation. In relation to plant height, a quantitative trait loci (QTL) was located in LG3, close to the Ts5 marker, that explained 29% of phenotypic variation. A QTL for 100-seed weight located in LG4, close to TA176, explained 51% of variation. The identification of a locus linked both to high 100-seed weight and days-to-flowering may account for the correlation observed between these traits in this and other breeding attempts.