Person: ATAK, ÇİMEN
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ATAK
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ÇİMEN
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Publication Restricted Comparison of Tolerance Related Proteomic Profiles of Two Drought Tolerant Tomato Mutants Improved by Gamma Radiation(Elsevier B.V., 2021) ÇELİK, ÖZGE; AYAN, ALP; MERİÇ, SİNAN; ATAK, ÇİMENLycopersicon esculentum L., also known as tomato, is an important industrial plant due to its products which worth billions of dollars annually, besides its nutritional value and health benefits. In this study, we investigated the two-dimensional protein expression profiles in drought tolerant mutant plants derived from industrial 5MX12956 tomato variety by Cs-137 gamma radiation source induced mutations. Drought tolerance of mutants were evaluated and confirmed by in vivo and in vitro methods. Eleven drought responsive protein spots were identified by two-dimensional electrophoresis and MALDI-TOF-MS. Identified proteins which presented differential expression under drought conditions were clustered under six distinct groups based on their cellular functions. These clusters are ATP and carbohydrate metabolism, mRNA processing and protein phosphorylation, oxidation reduction and stress response, signaling and supporting cytoskeleton. Our results contributed proteomic data to drought tolerance of our tomato mutants which were originated from drought susceptible 5MX12956 variety. They may also facilitate basis for future investigations into the genetic and physiological aspects of this tolerance. © 2021 Elsevier B.V.Publication Metadata only Heavy Metal Stress-Responsive Phyto-miRNAs(Springer Science and Business Media B.V., 2020) ÇELİK, ÖZGE; AYAN, ALP; MERİÇ, SİNAN; ATAK, ÇİMENHeavy metal stress is a leading abiotic stress factor in the twenty-first century as a reflection of industrial developments and extensive urbanization. Plants adopt several adaptation mechanisms to cope with deleterious effects of heavy metal stress. Biosynthesis of amino acids/organic acids, phytochelatins (PCs), metallothioneins (MTs), heat-shock proteins (HSPs), metal chelators, chaperons, ABC-type transporters, and CDF family metal transporters are among the heavy metal binding or transporting mechanisms in plants. This chapter emphasizes phyto-miRNAs related to these tolerance mechanism pathways. Moreover, transcription factors which are targeted by heavy metal-related phyto-miRNAs are also summarized under the effect of various heavy metals due to their intertwined regulatory mechanisms.Publication Metadata only Raman spectroscopic and chemometric investigation of lipid-protein ratio contents of soybean mutants(2020) Yılmaz, Ayberk; Kabuk, Hayrunnisa Nur; Kaygısız, Ersin; Fausto, Rui; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; ILDIZ, GÜLCE ÖĞRÜÇSeeds belonging to fourth generation mutants (M-4) of Ataem-7 cultivar (A7) variety and S04-05 (S) breeding line salt-tolerant soybeans were investigated by Raman spectroscopy, complemented by chemometrics methods, in order to evaluate changes induced by mutations in the relative lipid-protein contents, and to find fast, efficient strategies for discrimination of the mutants and the control groups based on their Raman spectra. It was concluded that gamma irradiation caused an increase in the lipid to protein ratio of the studied Ataem-7 variety mutants, while it led to a decrease of this ratio in the investigated S04-05 breeding line mutants. These results were found to be in agreement with data obtained by reflectance spectrum analysis of the seeds in the full ultraviolet to near-infrared spectral region and suggest the possibility of developing strategies where gamma irradiation can be used as a tool to improve mutant soybean plants targeted to different applications, either enriched in proteins or in lipids. Ward's clustering and principal component analysis showed a clear discrimination between mutants and controls and, in the case of the studied S-type species, discrimination between the different mutants. The grouping scheme is also found to be in agreement with the compositional information extracted from the analysis of the lipid-protein contents of the different samples.Publication Restricted Profile-Based Proteomic Investigation of Unintended Effects on Transgenic and Gamma Radiation Induced Mutant Soybean Plants(Springer, 2023) MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMEN; Arı, ŞuleGM risk assessments are crucial for determination and prevention of potential adverse effects through early detection and proper evaluation of intended and potential unintended changes in molecular breeding. In this context, the concept of 'substantial equivalence' has been suggested for the safety tests of GM products for many years. This study evaluated differences between four types of Glycine max crops; transgenic soybean, its non-transgenic counterpart, gamma induced soybean mutant and its parental line, at proteomic level in context of substantial equivalence. The results revealed the ratio of differentially expressed protein spots to total protein spots in mutants compared to their parental line was 50.7%. This ratio was 41.2% in transgenic plants compared to their counterparts. Scatter plot analysis presented those mutant plants showed a wider spread than transgenic plants in terms of distribution of proteins. It was determined that up-regulated proteins in mutant plants have various biological roles in processes such as development, stress response, photorespiration and ribosomal subunit assembly. In transgenic plants, upregulated proteins were shown to have diverse biological roles in processes such as ribosomal subunit assembly, electron transport, amino acid and nucleic acid metabolism and cell wall biogenesis. Although debate on the potential unintended effects focuses on GM organisms, our results point out that the plants that gained new characteristics by various breeding methods should be characterized in all aspects case-by-case.Publication Metadata only BABA Pre-Treatment Before Drought Stress Revealed Tolerance Related Proteomic Alterations in Rice(Wiley, 2022) YALÇIN, HM; MAYTALMAN, S.; İHVAN, YF; GÜMÜŞ, TAMER; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMENPublication Metadata only Biotic Stress-Tolerant Plants Through Small Rna Technology(Elsevier, 2020) ÇELİK, ÖZGE; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMENWith an increasing population around the world, the rapid loss of agricultural fields shows us the urgent importance of finding solutions to develop agricultural productivity. Besides industrialization, several effectors such as abiotic and biotic factors cause losses in crop productivity. Biotic factors threaten production and transportation of products worldwide. Bacteria, fungi, viruses, and oomycetes cause losses both pre- and postharvest. It is crucial to improve biotic stress-tolerant plants to overcome reduction in plant productivity. For many years, researchers focused on understanding plant defense mechanisms. Anatomical, physiological, and molecular adaptive mechanisms were investigated for several plant species. Besides the innate immunity mechanisms, including cross-talk, among the phytohormones to manage appropriate defense mechanisms against pathogens, new generation strategies in crop improvements are widely used in plant biotechnology. Although conventional breeding has importance in breeding new varieties, new technologies increase the possibility of success. Recently, new combinations of technologies have been proven effective to develop new cultivars. Small RNA technology is one of the developing crop improvement technologies relying on regulating specific genes together with their sequence identity. In this chapter, we focus on the small RNA technologies used in improvement of biotic stress-tolerant plants.Publication Restricted Investigation of Tos17 LTR Retrotransposon Movements in Rice (Oryza sativa L.) Under Nickel and Boron Stress(Springer Heidelberg, 2024) MERİÇ, SİNAN; AYAN, ALP; GÜNDÜZ, BURCU; ÖZPİRİNÇCİ, CAN; ÇELİK, ÖZGE; ATAK, ÇİMENHeavy metal and metalloid pollution caused by the industrialization became a leading stress factors for agricultural plants. The increase in the amount of nickel and boron in agricultural areas due to mining and increasing industrial activity is an important agricultural constraint. The difference between deficiency and toxicity levels of these heavy metal and metalloid is extremely critical. Nickel and boron are important micronutrients for plant growth, while they become toxic at critical densities. Plants exhibit different responses to these pollutants. It is essential to find specific biomarkers to discriminate the tolerant varieties to develop elite varieties. Transposable elements are known to have an efficient role against environmental stress factors. In this research, we evaluated the potential use of Tos17 retrotransposon movement as a molecular marker to identify the stress tolerances of two Oryza sativa L. varieties against nickel and boron pollutants.