Metal Bioaccumulation and Potential Health Risk Assessment in Different Tissues of Three Commercial Fish Species (Merluccius merluccius, Mullus barbatus, and Pagellus erythrinus) from Edremit Bay (Aegean Sea), Turkey.

Metal levels and potential health risk assessment in muscle, liver, and gills of three fish species (Merluccius merluccius, Mullus barbatus, and Pagellus erythrinus) from the Edremit Bay were investigated in spring and autumn 2015. Metal concentrations (Hg, Cd, Pb, Cr, Cu, Zn, Mn, and Fe), metal pollution index, and bioaccumulation factors in P. erythrinus were observed to be generally higher than those in M. barbatus and M. merluccius. Tissue was the main factor that might be responsible from the variations of metals in fish species according to ANOVA and PCA. Hg concentrations in M. barbatus and P. erythrinus were greater than threshold limits defined by international authorities; however, no carcinogenic risks were found for Cd and Pb levels. According to the results, the bay has been negatively influenced by human activities, and further research on monitoring of the biota and sediments is recommended for Edremit Bay and similar coastal areas under human pressure.

A comparative study of two HPLC methods for dissolved monosaccharide analysis in seawater using 2-amino benzamide and 2-amino pyrazine as pre-column derivatization reagents.

Two reversed-phase HPLC methods for molecular analysis of dissolved free monosaccharides in seawater were investigated comparatively by optimizing chromatographic separations and pre-column derivatization reactions. Monosaccharides derivatized with 2-amino benzamide or 2-amino pyrazine, and reduced with 2-picoline borane or 2-dimethylamino borane. According to results of optimization, separation performance, and detection limits, 2-amino benzamide method gave better results than 2-amino pyrazine method. Among 12 monosaccharides tested, it was possible to quantify glucose + galactose, galacturonic acid, glucuronic acid, xylose + arabinose, ribose, mannose, and N-acetyl-d-glucosamine with detection limits between 1.2 and 11 nM with intra-day repeatability of 2-9% and inter-day repeatability of 3-9%. The optimized method has the same level of detection limit with a widely used anion exchange chromatography method. Besides the preliminary results reported in this study, it may be possible to achieve higher sensitivity and to detect more monosaccharides by the use of shorter and narrow-bore columns at different polarities in further studies.

Seasonal variations of multi-biomarker responses to metals and pesticides pollution in M. galloprovincialis and T. decussatus from Homa Lagoon, Eastern Aegean Sea.

Biomarkers (CAT, SOD, GPx, and AChE) were investigated in hepatopancreas and soft tissues of mussels (Mytilus galloprovincialis) and clams (Tapes decussatus) in response to metal and pesticide pollutions in Homa Lagoon. Mussel and clam samples were seasonally collected in January, May, August and November 2015. According to the results, higher metal concentrations determined in the soft tissues of both species in January. Hepatopancreas was found to accumulate higher levels of metals than soft tissue. Metal deposition potential in clams were higher than mussels. Pesticide levels were below detection limits in clams. In mussels, only 4,4'-DDE was detected in soft tissues and hepatopancreas in November. Highest AChE, CAT, SOD and GPx activities in mussels were determined in January. On the other hand, maximum AChE and CAT activities in clams were found in November. Seasonal variations of metals and biomarker levels might be related to species-specific physiology and environmental conditions.

Distributions and Sources of PAHs and OCPs in Surficial Sediments of Edremit Bay (Aegean Sea).

In this study, levels, distributions, and sources of polycyclic aromatic hydrocarbons (18 compounds) and organochlorine pesticides (19 compounds) in surface sediments of 14 stations from Edremit Bay (Aegean Sea) were investigated in April and November 2015. ΣPAH concentrations (0.65-175 ng/g) in Edremit Bay sediments indicated low pollution. ΣPAH levels were decreased in the order of inner (81.1 ± 47.0 ng/g), northern (48.4 ± 15.9 ng/g), and southern (19.0 ± 15.8 ng/g) bays. p,p'-DDE was the only organochlorine pesticide detected in Edremit Bay sediments and found between nd to 1.16 ng/g dw. According to sediment quality guidelines, PAHs and p,p'-DDE levels in Edremit Bay were below the threshold effect level, effect range low, and threshold effect concentration limits and the sediments have no potential ecological risks. Two- to 3-ring PAHs were found at higher levels than 4- to 5-ring PAHs. Molecular PAHs ratios and Principal Component Analysis-Multiple Linear Regression analyses indicated combustion of wood-coal and vehicle emissions might have contributed to PAH levels in the bay.

The Topology Prediction of Membrane Proteins: A Web-Based Tutorial.

There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics. The tutorial is based on step-by-step explanations with illustrations. It can be applied under supervision of an instructor in the lessons, or it can be used as a self-study guide by students. In the tutorial, membrane-spanning regions and α-helices of membrane proteins were predicted by internet-based bioinformatics tools. According to the results achieved from internet-based bioinformatics tools, the algorithms and parameters used were effective on the accuracy of prediction. The importance of this laboratory tutorial lies on the facts that it provides an introduction to the bioinformatics and that it also demonstrates an in silico laboratory application to the students at natural sciences. The presented example education material is applicable easily at all departments that have internet connection. This study presents an alternative education material to the students in biochemistry laboratories in addition to classical laboratory experiments.

Synthesis of new ibuprofen derivatives with their in silico and in vitro cyclooxygenase-2 inhibitions.

Cyclooxygenase-2 (COX-2) is one of the important targets for treatment of inflammation related diseases. In the literature, most of drug candidates are first synthesized and then their COX-2 inhibitory activities are tested by in vitro and in vivo experiments. However, synthesis of dozens of drug analogues without any interpretations on their inhibitory activity can result in loss of time and chemicals. Therefore, synthetic drug designs with molecular modeling are of importance to synthesize selective drug candidates against inflammatory diseases. The synthesis of the novel ibuprofen derivatives through their in silico and in vitro COX-2 inhibitory activities were investigated in the present study. Starting from ibuprofen, ibuprofen amide and ibuprofen acyl hydrazone derivatives were synthesized. According to the results of the in silico molecular docking and in vitro enzyme inhibition studies, the synthesized novel ibuprofen derivatives have selective COX-2 inhibition, and molecule 3a and 3c were showed higher inhibition compared to ibuprofen. In conclusion, the newly synthesized ibuprofen derivatives can be used in model in vivo studies.

Molecular analysis of the KIT gene in gastrointestinal stromal tumors with novel mutations.

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. KIT gene mutations have great importance for GISTs. This study evaluated the relationship between KIT mutations and GIST clinicopathologic features to define region-specific and population-specific differences. Genomic DNA was extracted from 60 GISTs, and polymerase chain reaction was performed for KIT gene exons 9, 11, 13, and 17. Polymerase chain reaction amplicons were sequenced in both directions. This study represents the first mutation data of the KIT gene in GISTs from a Turkish population and reports novel mutations. The mutation rate in exon 11 (46.7%) was remarkably higher than those of the other exons (8.3% for exon 9; 11.7% for exon 13; 1.7% for exon 17). There was an association between malignancy potential and the presence of KIT mutations (odds ratio=3.18). Cases with mutations in codons W557-K558 in exon 11 had 11-fold greater risk of malignancy when compared with those without a mutation in this exon (odds ratio=11). We report different mutations than those previously reported, which emphasizes the importance of personalized medicine that could be empowered by the use of bioinformatics tools in the diagnostic process and therapeutic approaches.