Kaan Yilancioglu

Oxidative Stress Is a Mediator for Increased Lipid Accumulation in a Newly Isolated Dunaliella salina Strain

Green algae offer sustainable, clean and eco-friendly energy resource. However, production efficiency needs to be improved. Increasing cellular lipid levels by nitrogen depletion is one of the most studied strategies. Despite this, the underlying physiological and biochemical mechanisms of this response have not been well defined. Algae species adapted to hypersaline conditions can be cultivated in salty waters which are not useful for agriculture or consumption. Due to their inherent extreme cultivation conditions, use of hypersaline algae species is better suited for avoiding culture contamination issues. In this study, we identified a new halophilic Dunaliella salina strain by using 18S ribosomal RNA gene sequencing. We found that growth and biomass productivities of this strain were directly related to nitrogen levels, as the highest biomass concentration under 0.05 mM or 5 mM nitrogen regimes were 495 mg/l and 1409 mg/l, respectively. We also confirmed that nitrogen limitation increased cellular lipid content up to 35% under 0.05 mM nitrogen concentration. In order to gain insight into the mechanisms of this phenomenon, we applied fluorometric, flow cytometric and spectrophotometric methods to measure oxidative stress and enzymatic defence mechanisms. Under nitrogen depleted cultivation conditions, we observed increased lipid peroxidation by measuring an important oxidative stress marker, malondialdehyde and enhanced activation of catalase, ascorbate peroxidase and superoxide dismutase antioxidant enzymes. These observations indicated that oxidative stress is accompanied by increased lipid content in the green alga. In addition, we also showed that at optimum cultivation conditions, inducing oxidative stress by application of exogenous H2O2 leads to increased cellular lipid content up to 44% when compared with non-treated control groups. Our results support that oxidative stress and lipid overproduction are linked. Importantly, these results also suggest that oxidative stress mediates lipid accumulation. Understanding such relationships may provide guidance for efficient production of algal biodiesels.

Chemogenomics and orthology-based design of antibiotic combination therapies

Combination antibiotic therapies are being increasingly used in the clinic to enhance potency and counter drug resistance. However, the large search space of candidate drugs and dosage regimes makes the identification of effective combinations highly challenging. Here, we present a computational approach called INDIGO, which uses chemogenomics data to predict antibiotic combinations that interact synergistically or antagonistically in inhibiting bacterial growth. INDIGO quantifies the influence of individual chemical–genetic interactions on synergy and antagonism and significantly outperforms existing approaches based on experimental evaluation of novel predictions in Escherichia coli. Our analysis revealed a core set of genes and pathways (e.g. central metabolism) that are predictive of antibiotic interactions. By identifying the interactions that are associated with orthologous genes, we successfully estimated drug‐interaction outcomes in the bacterial pathogens Mycobacterium tuberculosis and Staphylococcus aureus, using the E. coli INDIGO model. INDIGO thus enables the discovery of effective combination therapies in less‐studied pathogens by leveraging chemogenomics data in model organisms.

Target-independent prediction of drug synergies using only drug lipophilicity.

Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency to exhibit drug interaction has not been systematically studied. We assembled physicochemical descriptors for a set of antifungal compounds (“drugs”) previously examined for interaction. Analyzing the relationship between molecular weight, lipophilicity, H-bond donor, and H-bond acceptor values for drugs and their propensity to show pairwise antifungal drug synergy, we found that combinations of two lipophilic drugs had a greater tendency to show drug synergy. We developed a more refined decision tree model that successfully predicted drug synergy in stringent cross-validation tests based on only lipophilicity of drugs. Our predictions achieved a precision of 63% and allowed successful prediction for 58% of synergistic drug pairs, suggesting that this phenomenon can extend our understanding for a substantial fraction of synergistic drug interactions. We also generated and analyzed a large-scale synergistic human toxicity network, in which we observed that combinations of lipophilic compounds show a tendency for increased toxicity. Thus, lipophilicity, a simple and easily determined molecular descriptor, is a powerful predictor of drug synergy. It is well established that lipophilic compounds (i) are promiscuous, having many targets in the cell, and (ii) often penetrate into the cell via the cellular membrane by passive diffusion. We discuss the positive relationship between drug lipophilicity and drug synergy in the context of potential drug synergy mechanisms.

Cytotoxic effect of extract from Dunaliella salina against SH-SY5Y neuroblastoma cells.

Cytotoxic effects of essential oils extracted from Dunaliella salina on SH-SY5Y human neuroblastoma cells were investigated in this study. GC-MS analysis was used for determination of the composition of essential oils found in Dunaliella salina extract. All experimented concentrations of Dunaliella salina extract on SH-SY5Y human neuroblastoma cells were significantly more cytotoxic than the tested concentrations of the extract on ECV304 human endothelial cells used as a control. Fifthy compounds were detected in GC-MS analysis of the extract, and five major compounds were predominantly found as follows: octadecanoic acid, methyl ester (27.43%); hexadecanoic acid, methyl ester (Cas) methyl palmitate (24.82%); 9,12,15-octadecatrienoic acid, ethyl ester, (Z,Z,Z)- (7.39%); octadecanoic acid (5.03%), pentadecanoic acid (3.60%). The cytotoxic activity of Dunaliella salina extract on SH-SY5Y human neuroblastoma cells might be due to high concentrations of octadecanoic acid and hexadecanoic acid. Furthermore, results indicate that the extract demonstrates some proliferative effect on ECV304 cells in a dose-dependent manner between 0.25 and 5 μg/ml. These results suggest that Dunaliella salina may have anticancer potential against human neuroblastoma cells.

Screening of new antileukemic agents from essential oils of algae extracts and computational modeling of their interactions with intracellular signaling nodes

Microalgae are very rich in bioactive compounds, minerals, polysaccharides, poly-unsaturated fatty acids and vitamins, and these rich constituents make microalgae an important resource for the discovery of new bioactive compounds with applications in biotechnology. In this study, we studied the antileukemic activity of several chosen microalgae species at the molecular level and assessed their potential for drug development. Here we identified Stichococcus bacillaris, Phaeodactylum tricornutum, Microcystis aeruginosa and Nannochloropsis oculata microalgae extracts with possible antileukemic agent potentials. Specifically we studied the effects of these extracts on intracellular signal nodes and apoptotic pathways. We characterized the composition of essential oils of these fifteen different algae extracts using gas chromatography-mass spectrometry (GC-MS). Finally, to identify potential molecular targets causing the phenotypic changes in leukemic cell lines, we docked a selected group of these essential oils to several key intracellular proteins. According to results of rank score algorithm, five of these essential oils analyzed might be considered as in silico plausible candidates to be used as antileukemic agents.

Rediscovery of historical Vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods

Anatolia played an important role in the diversification and spread of economically important Vitis vinifera varieties. Although several biodiversity studies have been conducted with local cultivars in different regions of Anatolia, our aim is to gain a better knowledge on the biodiversity of endangered historical V. vinifera varieties in the northern Adana region of southern Anatolia, particularly those potentially displaying viticulture characteristics. We also demonstrate the genetic relatedness in a selected subset of widely cultivated and commercialized V. vinifera collection cultivars, which were obtained from the National Grapevine Germplasm located at the Institute of Viticulture, Turkey. In the present study, microsatellites were used in narrowing the sample size from 72 accessions down to a collection of 27 varieties. Amplified fragment length polymorphisms were then employed to determine genetic relatedness among this collection and local V. vinifera cultivars. The unweighted pair group method with arithmetic mean cluster and principal component analyses revealed that Saimbeyli local cultivars form a distinct group, which is distantly related to a selected subset of V. vinifera collection varieties from all over Turkey. To our knowledge, this is the first study conducted with these cultivars. Further preservation and use of these potential viticultural varieties will be helpful to avoid genetic erosion and to promote continued agriculture in the region.

An Artificial Neural Network-Based Estimation of Bremsstarahlung Photon Flux Calculated by MCNPX

An Artificial Neural Network-Based Estimation of Bremsstarahlung Photon Flux Calculated by MCNPX H.O. Tekina,b,∗, T. Manici, E.E. Altunsoy, K. Yilancioglu and B. Yilmaz Uskudar University, Vocational School of Health Services, Radiotherapy Department, İstanbul, Turkey Usküdar University, Medical Radiation Research Center (USMERA), İstanbul, Turkey Uskudar University, Vocational School of Health Service, Medical Imaging Department, Istanbul, Turkey d Uskudar University, Faculty of Engineering and Natural Sciences, Molecular Biology and Genetics Department, İstanbul, Turkey Okan University, Faculity of Medicine, Department of Radiology, Istanbul, Turkey