Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 5Citation - Scopus: 10Removal of Pesticide Residues From Apple and Tomato Cuticle(Springer, 2023) Tari, Vinaya; Yalçın, Melis; Turgut, Nalan; Gökbulut, Cengiz; Mermer, Serhan; Sofuoğlu, Sait Cemil; Turgut, CaferPesticide residues are always an unsolved problem in the world despite all kinds of prevention measures. The present research work is based on a scientific hypothesis, i.e., The removal of average pesticide residue is inversely proportional to the thickness of cuticle. The effects of boron-containing products and plant-based surfactants were tested for the removal of five pesticides (lambda-cyhalothrin, chlorpyrifos, diflubenzuron, metaflumizone, acetamiprid) on tomatoes and apples. Boron-containing products were able to remove the pesticide residues on average between 58.0 and 72.6% in tomatoes and 33.2-58.8% in an apple. While plant-based surfactants removed residues on average between 58.5 and 66.6% in tomatoes and 41.0-53.2% in an apple. The highest removal rate was 72% with etidot at 1%. The solution of 1% C8-C10 provided 66.6% average removal for tomatoes. Less removal was achieved in apples. For an apple, Log K-ow and molecular mass (independent variables) were significant with p < 0.01, and the coefficient of determination (R-2) was > 0.87. However, the multiple linear regression analysis for ground colemanite was significant with R-2 of 0.96. In tomatoes, neither Log K-ow nor molecular mass as significant. The correlation was found between the physical and chemical properties of pesticides, but it is estimated that the thickness of the cuticle is effective in removing pesticides.Article Citation - WoS: 10Citation - Scopus: 12Novel Hybrid Adsorption-Electrodialysis (aded) System for Removal of Boron From Geothermal Brine(American Chemical Society, 2022) Altınbaş, Bekir Fırat; Orak, Ceren; Ökten, Hatice Eser; Yüksel, AslıA novel hybrid adsorption-electrodialysis (AdED) system to remove environmentally harmful boron from geothermal brine was designed and effective operating parameters such as pH, voltage, and flow rate were studied. A cellulose-based adsorbent was synthesized from glycidyl methacrylate (GMA) grafted cellulose and modified with a boron selective n-methyl-d-glucamine (NMDG) group and characterized with SEM-EDX, FT-IR, and TGA analyses. Batch adsorption studies revealed that cellulose-based adsorbent showed a remarkable boron removal capacity (19.29 mg/g), a wide stable operating pH range (2-10), and an adsorption process that followed the Freundlich isotherm (R2= 0.95) and pseudo-second-order kinetics (R2= 0.99). In the hybrid AdED system, the optimum operating parameters for boron removal were found to be a pH of 10, a voltage of 10 V, a flow rate of 100 mL/min, and an adsorbent dosage of 4 g/L. The presence of the adsorbent in the hybrid system increased boron removal from real geothermal brine (containing 199 ppm boron) from 7.2% to 73.3%. The results indicate that the designed AdED system performs better than bare electrodialysis for boron removal from ion-rich real geothermal brine while utilizing environmentally friendly cellulose-based adsorbent.Article Citation - WoS: 58Citation - Scopus: 59Assessment of Different Nanofiltration and Reverse Osmosis Membranes for Simultaneous Removal of Arsenic and Boron From Spent Geothermal Water(Elsevier, 2021) Jarma, Yakubu A.; Karaoğlu, Aslı; Tekin, Özge; Baba, Alper; Ökten, H.Eser; Tomaszewska, Barbara; Kabay, NalanOne of the factors that determine agricultural crops’ yield is the quality of water used during irrigation. In this study, we assessed the usability of spent geothermal water for agricultural irrigation after membrane treatment. Preliminary membrane tests were conducted on a laboratory-scale set up followed by mini-pilot scale tests in a geothermal heating center. In part I, three commercially available membranes (XLE BWRO, NF90, and Osmonics CK- NF) were tested using a cross-flow flat-sheet membrane testing unit (Sepa CF II, GE-Osmonics) under constant applied pressure of 20 bar. In part II, different spiral wound membranes (TR-NE90-NF, TR-BE-BW, and BW30) other than the ones used in laboratory tests were employed for the mini-pilot scale studies in a continuous mode. Water recovery and applied pressure were maintained constant at 60% and 12 bar, respectively. Performances of the membranes were assessed in terms of the permeate flux, boron and arsenic removals. In laboratory tests, the permeate fluxes were measured as 94.3, 87.9, and 64.3 L m?2 h?1 for XLE BWRO, CK-NF and NF90 membranes, respectively. The arsenic removals were found as 99.0%, 87.5% and 83.6% while the boron removals were 56.8%, 54.2%, and 26.1% for XLE BWRO, NF90 and CK-NF membranes, respectively. In field tests, permeate fluxes were 49.9, 26.8 and 24.0 L m?2 h?1 for TR-NE90-NF, BW30-RO and TR-BE-BW membranes, respectively. Boron removals were calculated as 49.9%, 44.1% and 40.7% for TR-BE-BW, TR-NE90-NF and BW30-RO membranes, respectively. Removal efficiencies of arsenic in mini-pilot scale membrane tests were all over 90%. Quality of the permeate water produced was suitable for irrigation in terms of the electrical conductivity (EC) and the total dissolved solids (TDS) for all tested membranes with respect to guidelines set by the Turkish Ministry of Environment and Urbanisation (TMEU). However, XLE BWRO, CK-NF and NF90 membranes failed to meet the required limits for irrigation in terms of boron and arsenic concentrations in the product water. The permeate streams of TR-BE-BW, TR-NE90-NF and BW30-RO membranes complied with the irrigation water standards in terms of EC, TDS and arsenic concentration while boron concentration remained above the allowable limit. © 2020 Elsevier B.V.Article Citation - WoS: 1Citation - Scopus: 2Trna Wobble Base Modifications and Boric Acid Resistance in Yeast: Boron-Resistant Deletion Mutants Induce the General Amino Acid Control Mechanism and Activate Boron Efflux(Pleiades Publishing, 2020) Uluisik, I.; Karakaya, H.C.; Koc, A.Abstract: Boric acid is essential for plants and has many vital roles in animals and microorganisms. However, its high doses are toxic to all organisms. We previously screened yeast deletion collections to identify boric acid-resistant and susceptible mutants to identify genes that play a role in boron tolerance. Here, we analyzed boron resistant mutants (elp1∆, elp3∆, elp6∆, ncs2∆, ncs6∆ and kti12∆) for their abilities to modulate the general amino acid control system (GAAC) and to induce boron efflux pump ATR1. The mutants analyzed in this study lack the genes that play roles in tRNA Wobble base modifications. We found that all of the boron resistant mutants activated Gcn4-dependent reporter gene activity and increased the transcript level of the ATR1 gene. Additionally, boron resistant cells accumulated less boric acid in their cytoplasm compared to the wild type cells upon boron exposure. Thus, our findings suggested that loss of wobble base modifications in tRNA leads to GAAC activation and ATR1 induction, which in turn reduced intracellular boron levels and caused boron resistance. © 2020, Pleiades Publishing, Inc.Article Citation - WoS: 14Citation - Scopus: 16Transcriptomic Analysis of Boron Hyperaccumulation Mechanisms in Puccinellia Distans(Elsevier Ltd., 2018) Öztürk, Saniye Elvan; Göktay, Mehmet; Has, Canan; Babaoğlu, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnnePuccinellia distans, common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were treated for three weeks with normal (0.5 mg L−1) and elevated (500 mg L−1) boron levels in hydroponic solution. Expressed sequence tags (ESTs) derived from shoot tissue were analyzed by RNA sequencing to identify genes up and down-regulated under boron stress. In this way, 3312 differentially expressed transcripts were detected, 67.7% of which were up-regulated and 32.3% of which were down-regulated in boron-treated plants. To partially confirm the RNA sequencing results, 32 randomly selected transcripts were analyzed for their expression levels in boron-treated plants. The results agreed with the expected direction of change (up or down-regulation). A total of 1652 transcripts had homologs in A. thaliana and/or O. sativa and mapped to 1107 different proteins. Functional annotation of these proteins indicated that the boron tolerance and hyperaccumulation mechanisms of P. distans involve many transcriptomic changes including: alterations in the malate pathway, changes in cell wall components that may allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.Article Citation - WoS: 219Citation - Scopus: 242The Importance of Boron in Biological Systems(Urban und Fischer Verlag GmbH und Co. KG, 2018) Uluışık, İrem; Karakaya, Hüseyin Çağlar; Koç, AhmetBoron is an essential element for plants and probably essential for human and animal health. Boron has a broad range of physiological effects on biological systems at low concentrations, whereas it is toxic to at high concentrations. Eventhough there are many studies on boron's biological effects and toxicity, more information is needed to understand the mechanisms of its action. The aim of the current work is to review boron's function, transport and toxicity in different biological systems.Article Citation - WoS: 12Citation - Scopus: 14Roles of Atr1 Paralogs Ymr279c and Yor378w in Boron Stress Tolerance(Elsevier Ltd., 2011) Bozdağ, Gönensin Ozan; Uluışık, İrem; Gülcüler, Gülce Sıla; Karakaya, Hüseyin Çağlar; Koç, AhmetBoron is a necessary nutrient for plants and animals, however excess of it causes toxicity. Previously, Atr1 and Arabidopsis Bor1 homolog were identified as the boron efflux pump in yeast, which lower the cytosolic boron concentration and help cells to survive in the presence of toxic amount of boron. In this study, we analyzed ATR1 paralogs, YMR279c and YOR378w, to understand whether they participate in boron stress tolerance in yeast. Even though these genes share homology with ATR1, neither their deletion rendered cells boron sensitive nor their expression was significantly upregulated by boron treatment. However, expression of YMR279, but not YOR378w, from the constitutive GAPDH promoter on a high copy plasmid provided remarkable boron resistance by decreasing intracellular boron levels. Thus our results suggest the presence of a third boron exporter, YMR279c, which functions similar to ATR1 and provides boron resistance in yeast.Article Citation - WoS: 48Citation - Scopus: 52Boron Stress Activates the General Amino Acid Control Mechanism and Inhibits Protein Synthesis(Public Library of Science, 2011) Uluışık, İrem; Kaya, Alaattin; Fomenko, Dmitri E.; Karakaya, Hüseyin Çağlar; Carlson, Bradley A.; Gladyshev, Vadim N.; Koç, AhmetBoron is an essential micronutrient for plants, and it is beneficial for animals. However, at high concentrations boron is toxic to cells although the mechanism of this toxicity is not known. Atr1 has recently been identified as a boron efflux pump whose expression is upregulated in response to boron treatment. Here, we found that the expression of ATR1 is associated with expression of genes involved in amino acid biosynthesis. These mechanisms are strictly controlled by the transcription factor Gcn4 in response to boron treatment. Further analyses have shown that boron impaired protein synthesis by promoting phosphorylation of eIF2α in a Gcn2 kinase dependent manner. The uncharged tRNA binding domain (HisRS) of Gcn2 is necessary for the phosphorylation of eIF2α in the presence of boron. We postulate that boron exerts its toxic effect through activation of the general amino acid control system and inhibition of protein synthesis. Since the general amino acid control pathway is conserved among eukaryotes, this mechanism of boron toxicity may be of general importance.Article Citation - WoS: 20Citation - Scopus: 20Genome-Wide Identification of Genes That Play a Role in Boron Stress Response in Yeast(Elsevier Ltd., 2011) Uluışık, İrem; Kaya, Alaattin; Ünlü, Ercan Selçuk; Avşar, Kadir; Karakaya, Hüseyin Çağlar; Yalçın, Talat; Koç, AhmetBoron is an essential micronutrient for plants and it is either necessary or beneficial for animals. Studies identified only few genes related to boron metabolism thus far and details of how boron is imported into cells and used in cell metabolism are largely unknown. In order to identify genes that play roles in boron metabolism, we screened the entire set of yeast haploid deletion mutants and identified 6 mutants that were resistant to toxic levels of boron, and 21 mutants that were highly sensitive to boron treatment. Furthermore, we performed a proteomic approach to identify additional proteins that are significantly up-regulated by boron treatment. Our results revealed many genes and pathways related to boron stress response and suggest a possible link between boron toxicity and translational control.Article Citation - WoS: 55Citation - Scopus: 64Identification of a Novel System for Boron Transport: Atr1 Is a Main Boron Exporter in Yeast(American Society for Microbiology, 2009) Kaya, Alaattin; Karakaya, Hüseyin Çağlar; Fomenko, Dmitri E.; Gladyshev, Vadim N.; Koç, AhmetBoron is a micronutrient in plants and animals, but its specific roles in cellular processes are not known. To understand boron transport and functions, we screened a yeast genomic DNA library for genes that confer resistance to the element in Saccharomyces cerevisiae. Thirty boron-resistant transformants were isolated, and they all contained the ATR1 (YML116w) gene. Atr1 is a multidrug resistance transport protein belonging to the major facilitator superfamily. C-terminal green fluorescent protein-tagged Atr1 localized to the cell membrane and vacuole, and ATR1 gene expression was upregulated by boron and several stress conditions. We found that atr1△ mutants were highly sensitive to boron treatment, whereas cells overexpressing ATR1 were boron resistant. In addition, atr1△ cells accumulated boron, whereas ATR1-overexpressing cells had low intracellular levels of the element. Furthermore, atr1△ cells showed stronger boron-dependent phenotypes than mutants deficient in genes previously reported to be implicated in boron metabolism. ATR1 is widely distributed in bacteria, archaea, and lower eukaryotes. Our data suggest that Atr1 functions as a boron efflux pump and is required for boron tolerance.