Person: AYAN, ALP
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Dr. Öğr. Üyesi
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AYAN
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ALP
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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 Restricted Comparison of COVID-19 Laboratory Diagnosis by Commercial Kits: Effectivity of RT-PCR to the RT-LAMP(Wiley, 2022) ARTIK, YAKUP; Coşgun, Alp B.; Cesur, Nevra P.; Hızel, Nedret; Uyar, Yavuz; Sur, Haydar; AYAN, ALPCoronavirus disease 2019 or COVID-19 caused by novel coronavirus/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) is an ongoing pandemic that has emerging global effects and requires rapid and reliable diagnostic testing. Quantitative reverse transcription-polymerase chain reaction (q-RT-PCR) is the gold standard method for SARS-CoV-2 detections. On the other hand, new approaches remedy the diagnosis difficulties gradually. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) as one of these novel approaches may also contribute to faster and cheaper field-based testing. The present study was designed to evaluate this rapid screening diagnostic test that can give results in 30-45 min and to compare the effectiveness of LAMP to the q-RT-PCR. The 30 randomly chosen patient samples were generated by nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. The sample of quantification cycle (Cq) values was tested using RT-LAMP as well as by conventional q-RT-PCR. The patient samples were tested with four different kits (SENSObiz COVID-19 [SARS-CoV-2] LAMP Assay, the QIAseq DIRECT SARS-CoV-2 kit, Biospeedy SARS-CoV-2 Variant Plus kit, and CoVirion-CV19-2 SARS-CoV-2 OneStep RT-PCR kit) and two different PCR devices (GDS Rotor-Gene Q Thermocycler and Inovia Technologies GenX series). Based on 30 patient samples, the positive/negative ratio (P/N) was 30/0 as Biospeedy and Covirion (positivity 100%), 28/2 as Qiagen kit (positivity 93.3%) for the samples studied on the Inovia device while the same samples on the Rotor-Gene device were 30/0 as Biospeedy and Covirion (positivity 100%), 29/1 as Qiagen kit at the first day (96.7%). On the fifth day, the samples were studied in the Inovia device and the respective results were obtained: 27/3 as Biospeedy (positivity 90%), 16/14 as Qiagen (positivity 53.3%), 28/2 as Covirion kit (positivity 93.3%). When these samples were studied in the Rotor-Gene device, it was 29/1 in Biospeedy and Covirion (positivity 96.7%), 19/11 in the Qiagen kit (positivity 63.3%). When these samples were compared with the LAMP method it was found to be 19/11 (positivity 63.3%) on the first day and 18/12 (positivity 60%) on the fifth day. SARS-CoV-2 test studies will contribute to a proactive approach to the development of rapid diagnosis systems. The LAMP approach presents promising results to monitor exposed individuals and also improves screening efforts in potential ports of entry.Publication Metadata only Antioxidative defense system differences to drought stress of tomato cultivars(2014) AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; 185510; 113987; 6653Publication 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 Antioxidative defense system differences to drought stress of tomato cultivars(Elsevier Science Bv, Po Box 211, 1000 Ae Amsterdam, Netherlands, 2014-09) AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; 185510; 113987; 6653The aim of this study is to investigate the enzymatic and non-enzymatic responses of two different industrial tomato varieties (X5671R and 5MX12956) against drought stress. Fourteen-day-old seedlings were subjected to drought stress by non-watering and the stress was continued for 7 days. The effects of drought stress on tomato varieties analysed due to the results of biochemical analysis (total protein content, lipid peroxidation, relative water content, chlorophyll contents) and enzymatic activity and isozyme analysis of SOD, CAT, APX and POX. The highest water loss was recorded in X5671R as 73.17%. 64% total chlorophyll decrease was observed in both varieties on 7th day. Total protein, proline, malondialdehyde concentrations and antioxidant enzymes presented increase with related to increasing drought stress for both varieties. Due to the results, we concluded that 5MX12956 variety is more drought tolerant then X5671R. Isozyme densities and band differences were recorded. The densities of POX isozymes were started to increase from 5th day of stress. Fe-SOD, Cu/Zn-SOD1-2 isozyme bands were identified in X5671R variety, while 5MX12956 showed only Cu/Zn-SOD isozyme band. Differences in APX isozymes were observed from the 4th day of drought stress in both varieties. The results indicated the differences in antioxidant metabolism of tomato plants.Publication Metadata only Investigation of Tos-17 transposon mobility in salt stressed rice (Oryza sativa L.) plants by IRAP method(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2017-08-30) Gündüz, Burcu; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; 219257; 113987; 185510; 6653Publication 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 Embargo Enzymatic and non-enzymatic comparison of two different industrial tomato (Solanum lycopersicum) varieties against drought stress(Springer, 233 Spring St, New York, Ny 10013 USA, 2017-08-02) AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; 113987; 185510; 6653Background: The aim of this study is to compare the tolerance mechanisms of two industrial tomato varieties (X5671R and 5MX12956) under drought stress. 14 days-old tomato seedlings were subjected to 7 days-long drought stress by withholding irrigation. The effects of stress were determined by enzymatic and non-enzymatic parameters. The physiological damages were evaluated via lipid peroxidation ratio, total protein content, relative water content, chlorophyll content and proline accumulation. Enzymatic responses were determined by biochemical analysis and electrophoresis of SOD, APX, POX and CAT enzymes. Results: Relative water contents of X5671R and 5MX12956 varieties at 7th day of drought were decreased to 8.4 and 12.2%, respectively. Applied drought decreased all photosynthetic pigments of X5671R and 5MX12956 varieties during the treatment period significantly comparing to the Day 0 as the control. Total protein content, lipid peroxidation and proline accumulation presented increased values in both varieties in accordance with the increasing stress intensity. According to lipid peroxidation analysis, 5MX12956 tomato variety was found more drought sensitive than X5671R variety. Antioxidative enzyme activities showed increases in both varieties as a response to drought stress, although CAT and APX activities presented decrease on the 7th day of applied stress. 7 days long drought stress differentially altered POX, APX and SOD isozyme patterns. Same POX bands were observed in both varieties with different band intensities. Conclusions: However, main isozyme pattern differences were obtained for SOD and APX. APX1, Fe-SOD and Cu/Zn-SOD2 isozyme bands should be evaluated to define their main role in the tolerance mechanism of both tomato varieties.