In silico identification of novel lncRNAs with a potential role in diagnosis of gastric cancer

Abstract

Gastric cancer (GC) is the second leading cause of cancer-related deaths in the world. Due to the shortage of adequate symptoms in the early stages, it is diagnosed when the tumor has spread to distant organs. Early recognition of GC enhances the chance of successful treatment. Molecular mechanisms of GC are still poorly understood. LncRNAs are emerging as new players in cancer in both oncogene and tumor suppressor roles. High-throughput technologies such as RNA-Seq, have revealed thousands of lncRNAs which are dysregulated in GC. In this study, we retrieved lncRNAs obtained by High-throughput technologies from OncoLnc database. Consequently, retrieved lncRNAs were compared in literature-based databases including PubMed. As a result, two lists, including experimentally validated lncRNAs and predicted lncRNAs were provided. We found 43 predicted lncRNAs that had not been experimentally validated in GC, so far. Further Bioinformatics analyses were performed to obtain the expression profile of predicted lncRNAs in tumor and normal tissues. Also, the roles and targets of predicted lncRNAs in GC were identified by related databases. Finally, using the GEPIA database was reviewed the significant relationship of predicted lncRNAs with the survival of GC patients. By recognizing the lncRNAs involved in initiation and progression of GC, they may be considered as potential biomarkers in the GC early diagnosis or targeted treatment and lead to novel therapeutic strategies.

Communicated by Ramaswamy H. Sarma     

The effect of Candida cell wall beta-glucan on treatment-resistant LL/2 cancer cell line: in vitro evaluation

Candida albicans (C. albicans) cell wall beta-glucan has been considered as a potential agent in the treatment of cancers due to its anti-tumor properties. Therefore, in the present study, we investigated the anti-cancer effects of Candida cell wall beta-glucan on Lewis lung carcinoma cell line (LL/2) cells. Beta-glucan of C. albicans cell wall was extracted. LL/2 cell line was cultured, then sphere cells and parental cells were exposed to the different concentrations of beta-glucan extracted from C. albicans (10–6000 μg/ml), for 24, 48 and 72 h. Cytotoxicity of beta-glucan was assayed by MTT test, then RNA extracted from cells population (treated and untreated cells), cDNA synthetized and expression level of Sox2, Oct4, C-myc, Nanog genes were also investigated using Real-time methods. At optimal concentrations of 800 and 1000 μg/ml, the extracted beta-glucan showed a significant cytotoxic effect on both parental and sphere cell populations (p?<?0.05). Real-time PCR analysis revealed a decreased expression of Oct4 and Sox2 genes in treatment of cells with beta-glucan compared with control group. Since the extracted beta-glucan showed an inhibitory effect on the expression of Oct4 and Sox2 genes involved in LL/2 metastasis, therefore, beta-glucan can be considered as an anti-tumor agent because of its anti-metastatic properties, however, more in vitro and in vivo studies are needed to provide further evidence on this topic in the future.

     

Immobilization of HIV-1 TAT peptide on gold nanoparticles: A feasible approach for siRNA delivery

RNA interference is one of the prosperous approaches for cancer treatment. However, small interfering RNA (siRNA) delivery to cancer cells has been faced with various challenges restricting their clinical application over the decades. Since ROR1 is an onco-embryonic gene overexpressed in many malignancies, suppression of ROR1 by siRNA can potentially fight cancer. Herein, a delivery system for ROR1 siRNA based on HIV-1 TAT peptide-capped gold nanoparticles (GNPs) was developed to treat breast cancer. Besides, we introduced a new feasible method for conjugating the peptide to the nanoparticles. Since the GNPs have high affinity to the sulfur, the findings demonstrated the peptide successfully conjugated to the nanoparticles via Au–S bonds. As positively charged nanoparticles showed high cellular uptake, we could use a low concentration of nanoparticles led to high efficient gene transfection with negligible cytotoxicity that was confirmed by flow cytometry, confocal microscopy, gel retardation, and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Following transfection, downregulation of ROR1 and its targeted gene, CCND1, induced apoptosis in cancer cells. In conclusion, the reported capped GNPs could be potentially utilized for delivering negatively charged therapeutic agents in particular genes.     

Natural parasitism of the diamondback moth,Plutella xylostella (L.) (Lep.: Plutellidae) by a larval parasitoid wasp,Diadegma anurum on different cauliflower cultivars

The diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Yponomeutidae), is the most serious pest of cauliflower fields in central Iran and its control is primarily based on pesticide sprays. Over the past years, a number of new pesticide compounds were introduced onto the market and some of them may cause adverse effects on natural populations of parasitoids associated with DBM. Excessive use of insecticides against the pest did not produce satisfactory results but has caused concerns about environmental pollution and increased pest resistance to chemicals. This research aims to study natural parasitism of pest on different cauliflower cultivars in the fields of south of Tehran. Dominant species of parasitoids include Diadegma anurum, Cotesia plutellae and Oomyzus sokolowskii. The highest parasitism rate was observed by D. anurum that was recorded on Buris cultivar (19.92?±?1.06) and White cloud cultivar (16.20?±?1.49) and the lowest parasitism rate was observed on Snow crown cultivar (3.42) and SG cultivar (5.00) during the season.     

Screening of oilseed rape cultivars relation to diamondback moth,Plutella xylostella (Lep.: Plutellidae) in fields of Tehran

The diamondback moth (DBM), Plutella xylostella (L.) (Lep., Plutellidae), is one of the most important pests of oilseed rape, Brassica napus L., in the world. In this study, resistance of oilseed rape cultivars to DBM was evaluated in fields of Tehran based on injury rate of the cultivars. To evaluate cultivar resistance, 19 cultivars of oilseed rape were planted in randomised complete-block design with three replications. Total experiments were conducted in experimental field of Shahed University. Results showed that DBM had activity on the plants during season and peak of the injury occurred on 27 May. Results indicated that the total of oilseed rape cultivar was spotty. Statistical analysis showed that there was significant difference among determined characteristics in all cultivars. The highest and lowest numbers of holes in the leaf were observed in Midas, Karaj3, Zarfam and Hyola420, Hyola308 cultivars, respectively, in sampling of the end growth. Opera and Midas cultivars have the highest percentage of leaf infestation and the lowest percentage of leaf infestation was observed in Hyola420 and Hyola308. Also, Karaj3 and Zarfam cultivars have the highest percentage of meristem infestation and the lowest percentage of meristem infestation was observed in Licard and Hyola420 cultivars. Based on peak of the injury rate and importance of meristem injury, Hyola420 and Hyola308 cultivars were relatively resistant to DBM, and Karaj3 and Zarfam were relatively sensitive to DBM.     

Efficient growth inhibition of EGFR over-expressing tumor cells by an anti-EGFR nanobody

Epidermal growth factor receptor (EGFR) is deemed to be one of the main molecular targets for diagnosis and treatment of cancer. It has been identified that EGFR involves in pathogenesis of some forms of human cancers. Monoclonal antibodies targeting EGFR could control the tumor cell growth, proliferation, and apoptosis by suppressing the signal transduction pathways. Nanobodies can be regarded as the smallest intact antigen binding fragments, derived from heavy chain-only antibodies existing in camelids. Here, we describe the identification of an EGFR-specific nanobody, referred to as OA-cb6, obtained from immunized camel with a cell line expressing high levels of EGFR. Utilizing flow cytometry (FACS) and blotting methods, we demonstrated that OA-cb6 nanobody binds specifically to EGFR expressing on the surface of A431 cells. In addition, OA-cb6 nanobody potently causes the inhibition of EGFR over expression, cell growth and proliferation. The antibody fragments can probably be regarded as worthwhile binding block for further rational design of anti-cancer therapy.     

Conformational behaviours of 2-substituted cyclohexanones: a complete basis set,hybrid-DFT study and NBO interpretation

The generalised anomeric effect (GAE) and gauche effect (GE) associated with donor–acceptor delocalisations, dipole–dipole interactions and total steric exchange energies (TSEE) on the conformational properties of 2-methoxy- (1), 2-methylthio- (2), 2-methylseleno- (3), 2-fluoro- (4), 2-chloro- (5) and 2-bromocyclohexanone (6) have been studied by means of ab initio and hybrid density functional theory methods and natural bond orbital (NBO) analysis. All methods used showed that the axial conformation stability increased from 2-methoxy- (1) to 2-methylselenocyclohexanone (3) and also from 2-fluoro- (4) to 2-bromocyclohexanone (6), which is in agreement with reported NMR data. The results obtained by complete basis set 4 (CBS-4), B3LYP/6-311+G** and HF/6-311+G** levels for compounds 1, 5 and 6 are very similar, but the CBS-4 results for compound 4 are not in agreement with the reported experimental data (vapour phase). The NBO analysis showed that the GAE increases from compounds 1 to 3 and also from compounds 4 to 6. The low axial conformer populations of compounds 1 and 4 can be reasonably explained by their small GAE. GE does not have significant impact on the conformational behaviours of compounds 1–6 and GAE succeeds in accounting qualitatively for the increase in the axial preferences in both series of compounds. The results showed that the calculated Δ(TSEE_eq–ax) values decrease from compounds 4 to 6 which contradicts the suggested arguments in the literature about these compounds. On the other hand, the calculated differences between the dipole moment values of the axial and equatorial conformations, Δ(μ_eq ? μ_ax), increase from compounds 1 to 2, but decrease from compounds 2 to 3 and also decrease from compounds 4 to 6. The calculated GAE values are more significant for the explanation of the conformational preferences of compounds 1–6 than the dipole–dipole repulsion effects. The correlations between the GAE, GE, dipole–dipole interactions, Wiberg Bond Index, TSEE, donor and acceptor orbital energies and occupancies, structural parameters and conformational behaviour of compounds 1–6 have been investigated.     

Adsorption of Basic violet 16 from aqueous solutions by waste sugar beet pulp: kinetic,thermodynamic, and equilibrium isotherm studies

Waste sugar beet pulp has been used as adsorbent for the removal of a hazardous cationic dye, Basic violet 16, from its aqueous solution. Adsorption of the dye was studied as function of time, pH of the solution, dosage of the adsorbent, sieve size of the particles, concentration of the dye, and temperature. The initial pH of the dye solution did not affect the chemistry of the dye molecule and the surface of beet pulp. Langmuir and Freundlich adsorption isotherms were successfully employed, and on the basis of these models, the thermodynamic parameters were evaluated. Adsorption of Basic violet 16 on beet pulp was found to be an exothermic reaction. Time contact studies showed that more than 80% adsorption of the dye is achieved in less than 1 h. Kinetics investigations confirmed both pseudo-first-order and pseudo-second-order behaviors; on the other hand, it shows that the intraparticle diffusion step is not the only rate-controlling step in all concentrations.     

Exploiting Edge Effect to Control Generation Rate and Breakdown Voltage in Graphene Nanoribbon Field Effect Transistors

Plasmonics - Based on the influence of edge effect and channel shape, two new graphene nanoribbon field effect transistors are presented being useful in high-voltage and highly sensitive optical...