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    Computational screening of dipeptidyl peptidase IV inhibitors from micoroalgal metabolites by pharmacophore modeling and molecular docking
    (Wiley, 2016) Selvaraj, Gurudeeban; Kaliamurthi, Satyavani; Cakmak, Zeynep E.; Cakmak, Turgay
    Dipeptidyl peptidase IV (DPP-IV) catalyzes conversion of GLP1 (glucagon like peptide 1) to inert structure, which results in insufficient secretion of insulin and increase in postprandial blood glucose level. The present study attempts to identify novel inhibitors from bioactive metabolites present in microalgae against DPP-IV through virtual screening, molecular docking, and pharmacophore modeling for the active target. Possible binding modes of all 60 ligands against DPP-IV receptor were constructed using MTiOpenScreen virtual screening server. Pharmacophore model was built based on identified 38 DPP-IV test ligands by using the web-based PharmaGist program which encompasses hydrogen-bond acceptors, hydrophobic groups, spatial features, and aromatic rings. The pharmacophore model having highest scores was selected to screen active DPP-IV ligands. Highest scoring model was used as a query in ZincPharmer screening. All identified ligands were filtered, based on the Lipinski's ruleof- five and were subjected to docking studies. In the process of docking analyses, we considered different bonding modes of one ligand with multiple active cavities of DPP-IV with the help of AutoDock 4.0. The docking analyses indicate that the bioactive constituents, namely, beta-stigmasterol, barbamide, docosahexaenoic acid, arachidonic acid, and harman showed the best binding energies on DPP-IV receptor and hydrogen bonding with ASP545, GLY741, TYR754, TYR666, ARG125, TYR547, SER630, and LYS554 residues. This study concludes that docosahexaenoic acid, arachidonic acid, beta-stigmasterol, barbamide, harman, ZINC58564986, ZINC56907325, ZINC69432950, ZINC69431828, ZINC73533041, ZINC84287073, ZINC69849395, and ZINC10508406 act as possible DPP-IV inhibitors.
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    Induction of triacylglycerol production in Chlamydomonas reinhardtii: Comparative analysis of different element regimes
    (Elsevier Sci Ltd, 2014) Cakmak, Zeynep E.; Olmez, Tolga T.; Cakmak, Turgay; Menemen, Yusuf; Tekinay, Turgay
    In this study, impacts of different element absence (nitrogen, sulfur, phosphorus and magnesium) and supplementation (nitrogen and zinc) on element uptake and triacylglycerol production was followed in wild type Chlamydomonas reinhardtii CC-124 strain. Macro- and microelement composition of C. reinhardtii greatly differed under element regimes studied. In particular, heavy metal quotas of the microalgae increased strikingly under zinc supplementation. Growth was suppressed, cell biovolume, carbohydrate, total neutral lipid and triacylglycerol levels increased when microalgae were incubated under these element regimes. Most of the intracellular space was occupied by lipid bodies under all nutrient starvations, as observed by confocal microscopy and transmission electron micrographs. Results suggest that sulfur, magnesium and phosphorus deprivations are superior to nitrogen deprivation for the induction triacylglycerol production in C. reinhardtii. On the other hand, FAME profiles of the nitrogen, sulfur and phosphorus deprived cells were found to meet the requirements of international standards for biodiesel. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.
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    Nitrogen and sulfur deprivation differentiate lipid accumulation targets of Chlamydomonas reinhardtii
    (Landes Bioscience, 2012) Cakmak, Turgay; Angun, Pinar; Ozkan, Alper D.; Cakmak, Zeynep; Olmez, Tolga T.; Tekinay, Turgay
    Nitrogen (N) and sulfur (S) have inter-related and distinct impacts on microalgal metabolism; with N starvation having previously been reported to induce elevated levels of the biodiesel feedstock material triacylglycerol (TAG), while S deprivation is extensively studied for its effects on biohydrogen production in microalgae. 1,2 We have previously demonstrated that N- and S-starved cells of Chlamydomonas reinhardtii display different metabolic trends, suggesting that different response mechanisms exist to compensate for the absence of those two elements. 3 We used C. reinhardtii CC-124 mt(-) and CC-125 mt(+) strains to test possible metabolic changes related to TAG accumulation in response to N and S deprivation, considering that gamete differentiation in this organism is mainly regulated by N. 4 Our findings contribute to the understanding of microalgal response to element deprivation and potential use of element deprivation for biodiesel feedstock production using microalgae, but much remains to be elucidated on the precise contribution of both N and S starvation on microalgal metabolism.
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    Production and characterization of spherical thermostable silver nanoparticles from Spirulina platensis (Cyanophyceae)
    (Taylor & Francis Ltd, 2016) Kaliamurthi, Satyavani; Selvaraj, Gurudeeban; Cakmak, Zeynep Elibol; Cakmak, Turgay
    Biological production of silver nanoparticles (SNP) has recently received considerable attention because of their therapeutic applications. The present study reports the production and characterization of spherical-thermostable SNP from Spirulina platensis. Wet biomass harvested from optimized logarithmic-phase culture was used for production of SNP in 1, 3, or 5 mM silver nitrate solution. Formation and concentration of spherical SNP was highest when S. platensis was treated with 3 mM silver nitrate. Fourier transform infrared spectra of SNP indicate that vanillin, coumarins, tannins, amide, and glycogen may act as stabilizing agents for bioreduction. The crystalline nature of the produced SNP was evidenced from X-ray diffractometer analysis. Weight loss of SNP occurred at 210 degrees C, 310 degrees C, and 510 degrees C as shown by thermogravimetric analysis. This study shows that S. platensis may be used as an efficient tool for production of spherical, crystalline, and thermostable SNP.
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    Two pronounced Chlorella strains for efficient biodiesel feedstock production
    (Tubitak Scientific & Technical Research Council Turkey, 2019) Tuzun, Ilhami; Cakmak, Zeynep Elibol; Young, Emmanuel; Cakmak, Turgay
    In this study, two indigenous Chlorella strains were evaluated for triacylglycerol (TAG) production and related parameters during 10 days of N-deprivation. The strains were identified based on morphological characteristics and genomic information, named as Chlorella sp. IMU12 and Chlorella sp. IMU17. Time-dependent reduction of growth was accompanied by decreased chlorophyll content, reduced oxygen evolution ratio, and elevated carotenoid content of both strains cultivated in N-free Bold's basal medium. Nitrogen deprivation induced total lipid and neutral lipid content in both strains, supported by FTIR measurement of TAGs. Chlorella sp. IMU17 showed higher production of TAGs as a response to N-deprivation. Strikingly, relative polysaccharide content showed a rapid increase on the first days and a noticeable reduction was recorded especially after 5 days of N-deprivation while TAG production showed a gradual increase during the whole period of N-deprivation in both strains. Starch might be a predominant form of carbon storage in the short term and the continuous increase of TAG production might be supported by degradation of starch in a longer period of N-deprivation. FAME analysis of lipids showed that the saturation level of the fatty acids of both strains meets the European standard EN 14214 requirements. Lastly, N-deprivation stimulated a significant reduction of PUFA production in Chlorella sp. IMU17. Thus, Chlorella sp. IMU17 might stand as a promising candidate for biodiesel feedstock production with its low PUFA content and a concomitant induction of saturation of fatty acids as a clear response to N-deprivation.