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Now showing 1 - 10 of 17
  • Publication
    Genome organization changes in GM and non-GM soybean [Glycine max (L.) Merr.] under salinity stress by retro-transposition events
    (2020-04-09) Gözükırmızı, Nermin; Arı, Şule; Şahin, Olcay; Karlık, Elif; MERİÇ, SİNAN;
    Genetically modified (GM) crops are developed and cultivated worldwide, providing protection against insects and diseases, or tolerance to herbicides. However, despite the advantages that GM crops, they pose many concerns not only to human and animal health but also to the environment. In the present study, we perform inter-retrotransposon amplified polymorphism (IRAP)-PCR to reveal SIRE1, Bagy2 and Nikita transposition events in soybean [Glycine max (L.) Merr.] and GM soybean under increasing salt stress conditions (0 mM as control, 80 mm, 120 mM, 160 mM and 200 mM NaCl). Salinity dramatically affected soybean and GM soybean in a similar way that stem lengths, root lengths and leaf areas were reduced compared to control. According to IRAP-PCR results, polymorphism ratios of SIRE1, Bagy2 and Nikita retrotransposons among all samples were found to be 22–100%, 0–73% and 37–100%, respectively. These results are the first direct report to demonstrate the relationship between TEs polymorphisms and salinity stress in soybean and GM soybean. TEs, which may explain part of the new phenotypes, play essential roles in genome and gene evolution. Such information can be useful to understanding of genome organization differences derived from TEs between soybean and GM soybean.
  • Publication
    GMO analysis methods for food: From today to tomorrow
    (2017) Çakır, Özgür; Arı, Şule; MERİÇ, SİNAN
    In the last decades, the dynamic face of biotechnology increased the number of M plants and abled the production of more precise genetically modified organisms. Since the introduction of recently developed new breeding techniques, there has been on-going debate on food safely and on the regulation concern of new biotech crops. The presently used one-by-one approach for CMOs which has been commercialized and developed by mainly transforming the usage of a transgenic insert so far, is reorganized for legislation needs of these new organisms. Furthermore, the growing number of complexities of G MOs in the commercialization pipeline and the possibility of the presence of unauthorized CMOs in the food chain has led to a demand for new technologies and stratagies to detect CMOs. In order to provide readers with current viewpoints on this topic, this chapter focuses on the key points at present. These are developing biotech plants, analysis methods for food and feed in the light of new breeding technologies, and the unintended effects of genetic transformation. It will summarize the DNA-based polymerase chain reaction (PCR) technique, the most widely accepted GMO detection method, which is classified into screening, gene-specific, construct specific, and transgenic event-specific methods according to the level of specificity. 'ubsequently, this chapter will elaborate the envisaged evolution of the GMO crops and the challenge for the detection methods of new biotech crops.
  • Publication
    Heavy Metal Stress-Responsive Phyto-miRNAs
    (Springer Science and Business Media B.V., 2020) ÇELİK, ÖZGE; AYAN, ALP; MERİÇ, SİNAN; ATAK, ÇİMEN
    Heavy 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.
  • PublicationRestricted
    Comparison of Tolerance Related Proteomic Profiles of Two Drought Tolerant Tomato Mutants Improved by Gamma Radiation
    Lycopersicon 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
    Epigenetic analysis of WRKY Transcription Factor Genes in Salt Stressed Rice (Oryza sativa L.) plants
    (Elsevier, 2018) MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; 113987; 219257; 185510; 6653
    It is important for plants to survive when they are subjected to environmental stress factors under different combinations in nature. In such conditions, epigenetic modifications such as cytosine methylations have a regulatory role in adaptive responses to changing environment. WRKY transcription factor family is one of the largest families managing regulation of various processes in plants. Although, the WRKYs are known to play important regulatory role in stress tolerance, the exact mechanisms underlying for regulation of each member under different conditions are not clarrified yet. Among WRKY family members, WRKY50 and WRKY72 were reported to be differentially regulated under salt stress. In this study, we compared the level of cytosin methylation patterns of both WRKY transcription factors under different salt concentration treated Osmancık-97 rice variety (Oryza sativa L.) seedlings. DNA methylation status of both genes in leaf tissues of NaCl stressed (0, 30 mM, 90 mM, 150 mM and 210 mM) rice plants were assessed by bisulfite sequencing. The sequencing reads were mapped according to Oryza sativa genome (v.7). Principal Component Analysis and the Fisher’s exact test were performed to compare the levels of methylated cytosines in CpG in the samples. Differentially methylated cytosines were identified and comparatively analyzed by methylKit. A total of 155 MetCs positions in the CpG context were detected comparing all libraries. 72 methylated cytosines correspond to WRKY50 sequence and 83 methylated cytosines were detected in the WRKY72 region. The methylation levels of the WRKY genes were found in negative correlation with gene expression at 90 and 150 mM NaCl treatments, however at 210 mM concentration the data indicate more complex status of the relation.
  • Publication
    Lipid/Protein Ratio Contents of Soybean Mutants: A Raman Spectroscopic and Chemometrics Investigation
    (2018) Kabuk, Hayrunnisa; Kaygısız, Ersin; Rui, Fausto; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; ILDIZ, GÜLCE ÖĞRÜÇ; 107326; 113987; 6653; 175748; 185510; 219257
  • Publication
    Biotic Stress-Tolerant Plants Through Small Rna Technology
    With 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
    Investigation of horizontal gene transfer (HGT) from genetically modified plants to bacteria
    (Wiley-Blackwell, 111 River St, Hoboken 07030-5774, NJ USA, 2016-09) Özbilgiç, R.; Şahin, O.; Tombul, N.; Arı, Şule; MERİÇ, SİNAN; 219257; 2083
  • Publication
    Inducing salt tolerance in rice (Oryza sativa L.) varieties by gamma radiation
    (Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2017-08-30) MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; 185510; 113987; 219257; 6653
  • Publication
    Two-dimensional protein profiles of drought tolerant tomato (Solanum lycopersicum) mutants improved by gamma radiation
    (2017-08-30) Topçuoğlu, Burak; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; 185510; 113987; 219257; 6653