Is a single nucleotide polymorphism a risk factor for lung cancer in the matrix metalloproteinase-2 promoter?

We aimed to investigate the association of polymorphism frequencies of MMP-2 C1306T and MMP-2 plasma enzyme activity in lung cancer patients. In this study 300 genomic DNA (200 lung cancer patients + 100 no lung cancer) were analyzed. Polymorphisms were determined by using polymerase chain reaction-restriction fragment length polymorphism (RFLP) and electrophoresis. Plasma MMP-2 enzyme activity levels were measured by using ELISA. Sex, asbestos expose and smoking might be risk factors for lung cancer. The frequencies of C1306T genotypes in controls CC 65%, CT 32%, TT 3% and in patients CC 61%, CT 37%, TT2 % were found. It was determined that CC genotype frequency increase significantly in patients and controls. Plasma MMP-2 enzyme activity levels were increased in lung cancer patients according to controls. Finally, we claimed that determining of MMP-2 enzyme level can be used as a marker in lung cancer.     

Immunosuppressive Therapy in Patients with Aplastic Anemia: A Single-Center Retrospective Study

BackgroundAplastic anemia (AA) is a rare disease in which hematopoietic stem cells are severely diminished resulting in hypocellular bone marrow and pancytopenia. Etiology of AA includes auto immunity, toxins, infection, ionizing radiation, drugs and rare genetic disorders, but in the majority of cases no cause can be identified. In the present study we assessed response rate, survival, relapse and clonal evolution in patients with AA treated with immunosuppressive therapy.MethodsPatients with AA who received immunosuppressive therapy between May 1998 and September 2013 were included in this study. Patients with non-severe AA (NSAA) were treated with cyclosporine (CsA) and danazol while patients with severe AA (SAA) as well as patients with NSAA who progressed to SAA after beginning of the treatment, were candidates for receiving antithymocyte globulin in addition to CsA and danazol.ResultsAmong the 63 studied patients, 29 (46%) had NSAA and 34 (54%) had SAA. Three months after treatment, overall response was 58.6% in NSAA and 12.9% in patients with SAA. Survival of all patients at 5, 10 and 15 years were 73%, 55% and 49%, respectively. Survival rates were significantly higher in patients with NSAA compared to patients with SAA as well as in patients who responded at 6 months compared to non-responders. The relapse risk was 39.7% at 10 years. Relapse occurred in patients who discontinued the therapy more than those who continued taking CsA (p value<0.01). The risk of clonal evolution was 9.9% at 10 years and 22.8% at 15 years after treatment.ConclusionThis long-term retrospective study indicated that immunosuppressive therapy should be recommended to patients with AA. Also, our experience indicated that immunosuppressive therapy should not be discontinued after response to therapy in patients with both NSAA and SAA due to high risk of relapse. Low dose of CsA should be continued indefinitely.     

Tuning Optical Discs for Plasmonic Applications

We present simple physical and chemical procedures that allow tuning and modification of the topography of gratings present in optical storage discs into geometries optimal for grating coupled plasmon resonance excitation. After proper metal coating, the tuned surfaces exhibit sharp plasmon resonances that can be excited at wavelengths ranging from 260 nm to over 2.7 μm with relatively high quality factors. As an immediate exemplary application, use of such optimized gratings in aqueous medium for refractive index measurement is demonstrated.     

Genetic divergence of Octopus vulgaris species in the eastern Mediterranean

Nucleotide divergence in cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA was analyzed to determine interpopulational variation of common octopus (Octopus vulgaris) species sampled along eastern Mediterranean. Nucleotide composition and nucleotide pair frequency analyses of 440 individuals representing 11 populations were investigated. Estimation of evolutionary divergence between sequences was conducted using Tamura-Nei model. Considering 440 individuals, 35 (5%) variable sites and an average variation of 1.9% were found between specimens. Highest divergence was found between Med11 and Med04-Med07 populations; with a genetic distance value of 0.039 (3.9%). Estimation of transition/transversion bias (R) was made under the Tamura-Nei model and resulted as 2.32. Phylogenetic tree was constructed using four methods: neighbor joining (NJ), minimum evolution (ME), maximum likelihood (ML) and unweighted pair-group method of arithmetic average (UPGMA). Results from clustering patterns of the consensus tree, with the sum of branch length = 0.05189, pointed out a correlation between genetic and geographic distance.     

Application of an unsupervised artificial neural network technique to multivariant surface water quality data

Surface water contamination from agricultural and urban runoff and wastewater discharges from industrial and municipal activities is of major concern to people worldwide. Classical models can be insufficient to visualise the results because the water quality variables used to describe dynamic pollution sources are complex, multivariable, and nonlinearly related. Artificial intelligence techniques with the ability to analyse multivariant water quality data by means of a sophisticated visualisation capacity can offer an alternative to current models. In this study, the Kohonen self-organising feature maps (SOM) neural network was initially applied to analyse the complex nonlinear relationships among multivariable surface water quality variables using the component planes of the variables to determine the complex behaviour of water quality parameters. The dependencies between water quality variables were extracted and interpreted using the pattern analysis visualised in component planes. For further investigation, the k-means clustering algorithm was used to determine the optimal number of clusters by partitioning the maps and utilising the Davies–Bouldin clustering index, leading to seven groups or clusters corresponding to water quality variables. The results reveal that the concentrations of Na, K, Cl, NH₄-N, NO₂-N, o-PO₄, component planes of organic matter (pV), and dissolved oxygen (DO) were significantly affected by seasonal changes, and that the SOM technique is an efficient tool with which to analyse and determine the complex behaviour of multidimensional surface water quality data. These results suggest that this technique could also be applied to other environmentally sensitive areas such as air and groundwater pollution.     

Effects of poly(A)-binding protein on the interactions of translation initiation factor eIF4F and eIF4F.4B with internal ribosome entry site (IRES) of tobacco etch virus RNA

In wheat germ, the interaction between poly(A)-binding protein and eukaryotic initiation factor eIF 4G increases the affinity of eIF4E for the cap by 20-40-fold. Recent findings that wheat germ eIF4G is required for interaction with the IRES, pseudoknot 1 (PK1), of tobacco etch virus to promote cap-independent translation led us to investigate the effects of PABP on the interaction of eIF4F with PK1. The fluorescence anisotropy data showed addition of PABP to eIF4F increased the binding affinity approximately 2.0-fold for PK1 RNA as compared with eIF4F alone. Addition of both PABP and eIF4B to eIF4F enhance binding affinity to PK1 about 4-fold, showing an additive effect rather than the large increase in affinity shown for cap binding. The van't Hoff analyses showed that PK1 RNA binding to eIF4F, eIF4F.PABP, eIF4F.4B and eIF4F.4B.PABP is enthalpy-driven and entropy-favorable. PABP and eIF4B decreased the entropic contribution 65% for binding of PK1 RNA to eIF4F. The lowering of entropy for the formation of eIF4F.4B.PABP-PK1 complex suggested reduced hydrophobic interactions for complex formation. Overall, these results demonstrate the first direct effect of PABP on the interaction of eIF4F and eIF4F.4B with PK1 RNA.