Moleküler Biyoloji ve Genetik Bölümü / Department of Molecular Biology and Genetics
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Browsing Moleküler Biyoloji ve Genetik Bölümü / Department of Molecular Biology and Genetics by Publisher "Elsevier"
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Publication 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 Circulating MicroRNA Expression Profiles to Identify a Potential Link Between Prostate Cancer and Obesity(Elsevier, 2022) Arışan, Serdar; KILBAŞ, PELİN ÖZFİLİZ; RENCÜZOĞULLARI, ÖZGE; Ünsal, Narcin Palavan; Çoker-Gürkan, Ajda; Uysal-Onganer, Pınar; ARISAN, ELİF DAMLA; YERLİKAYA, PINAR OBAKANEffective diagnostic methods are needed to apply appropriate treatment strategies in patients with aggressive prostate cancer. From this point of view, risk factors that cause prostate cancer or its aggressiveness should be considered. Obesity is a critical risk factor for triggering prostate cancer's metastatic properties. microRNAs are used as biomarkers in diagnosing cancer and obesity depending on their tissue-specific expression patterns. This study investigates the role of obesity in the metastatic profile of prostate cancer depending on the differential expression signatures of selected miRNAs in prostate cancer and obese patients. The roles of miR-100, miR-141 and miR-145 in prostate cancer and obesity are partially known. However, their potential to become circular biomarkers in the blood is not elucidated. There is no previous data on miR-4463 and miR-653 on prostate cancer and obesity association. In this study, the blood samples were taken and obtained serum from 69 patients of 6 subgroups that consisted of one healthy group and five unhealthy groups based on their different prostate cancer or obesity levels. Five selected miRNA expression analyses (miR-100, miR-141, miR-145, miR-4463, and miR-653) were performed through total RNA isolation, which was confirmed via synthetic cel-miR-39 miRNA. Quantitative Real-Time PCR analyzed the expression levels of selected miRNAs. Data analysis was performed via normalising target miRNA expression levels with cel-miR-39. In this study, we found that the relationship between prostate cancer and obesity was investigated at the molecular level. It was suggested that target miR-100 could be a promising biomarker for non-obese and aggressive prostate cancer patients. miR-145 is a more potential biomarker than miR-141 for non-aggressive and non-obese patients. miR-4463 can be used to predict more prostate cancer patients than obese patients. Lastly, miR-653 can be a biomarker for non-aggressive prostate cancer cells.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; 6653It 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 MnSOD and IL-10 polymorphisms in chronic pelvic pain syndrome patients(Elsevier, 2006-04) Arısan, Serdar; Kiremit, Murat Can; Çaşkurlu, Turhan; Ünsal, Zeynep Narçin; Ergenekon, Erbil; ARISAN, ELİF DAMLA; 113920; 222920; 29912; 6125Publication Preparation of superoxide dismutase loaded chitosan microspheres: Characterization and release studies(Elsevier, 2007) Akbuğa, Fatma Jülide; ÇELİK, ÖZGE; 113987; 11241Superoxide dismutase (SOD) is the most potent antioxidant enzyme. In this study, SOD was encapsulated in chitosan microspheres to obtain suitable sustained protein delivery. Protein-loaded chitosan microspheres with various formulations were prepared based on complex coacervation process. Due to the inherent characteristic of SOD, high encapsulation efficiency could not be obtained with simple preparation method. The pH of chitosan solution is 3.0; when the chitosan microspheres were prepared with this solution, encapsulation was low. Therefore, several strategies have been tested to increase the encapsulation efficiency and good results have been obtained. 70–80% protein encapsulation efficiency was obtained. The addition of PEG to the protein solution enhanced the encapsulation efficiency also. Mean sizes of microspheres were between 1.38 and 1.94 μm. Factors affecting the release behaviour of SOD from microspheres have been studied. They included pH values of chitosan solution (the pH of chitosan solution is 3.0), addition of PEG to the protein solution and the use of adsorption technique. In general, biphasic release profiles were obtained with these formulations. The protein activity changed between 70 and 100% during the release. In general, the protein activity remained in acceptable limits. The SOD encapsulated chitosan microspheres can be prepared by changing the pH or addition of PEG, allowing the safe incorporation of protein for controlled release.Publication The Role of the PI3K/AKT/mTOR Signaling Axis in the Decision of the Celastrol-Induced Cell Death Mechanism Related to the Lipid Regulatory Pathway in Prostate Cancer Cells(Elsevier, 2020) RENCÜZOĞULLARI, ÖZGE; Çoban, Mervenur; Sevgin, Bortecine; Çoker-Gürkan, Ajda; YERLİKAYA, PINAR OBAKAN; Palavan-Ünsal, Narcin; ARISAN, ELİF DAMLAProstate cancer is one of the leading cancer types among the male population worldwide, with high incidence and mortality rates. Celastrol is a promising bioactive component extracted from Tripterygium wilfordi. Celastrol is a multimodal agent with therapeutic advantages, with activities that affect cell proliferation, inflammation (through affecting proteotoxic stress) and cell death mechanisms such as autophagy, apoptosis and paraptosis. Celastrol alters the PI3K/AKT signaling axis to suppress the cell viability of cancer cells. Although a number of celastrol targets have been identified in cancer cells, the genomic differences in malignant cells prevent the efficacy of celastrol. Therefore, new studies are required to highlight its potential therapeutic effects in cancer cells. In this study, we investigated the therapeutic potential of celastrol in LNCaP, DU145 and PC3 prostate cancer cells. According to our results, celastrol decreased cell viability in a dose-dependent manner in the cells. LNCaP prostate cancer cells were more sensitive to celastrol treatment compared to DU145 and PC3 cells. We found that celastrol modulated PI3K/AKT/mTOR signaling to alter lipid regulatory pathways by affecting LAMP -1 and lipin-1 in PC3 cells. Although celastrol downregulated FASN in all cell lines, active mTOR signaling led to altered responses in prostate cancer cells by affecting the cellular fate decision pathways.Publication Transcript profiling of salt tolerant tobacco mutants generated via mutation breeding(Elsevier, 2018-09) Ekşioğlu, Aybüke; Akdaş, Enes Yağız; ÇELİK, ÖZGE; 113987The main aim of the study is to identify the genes differentially, predominantly or specifically expressed in salt tolerant tobacco mutants, improved from Akhisar 97 and İzmir Özbaş varieties via mutation breeding, with respect to unstressed control plants. Seven tobacco mutants which have different salt tolerance capacities were evaluated by Gene Fishing analysis. Under stress conditions differentially expressed 100 reproducible bands were identified (74 of up-regulated and 20 of down-regulated while 6 were unknown). 75 of differentially expressed genes (DEGs) were successfully extracted from the gel and sequence analyses were performed. Functional annotation of the DEGs was performed against Blastn by interrogating their sequences. The 65 salt-regulated differentially expressed genes showed similarity with known genes, while 6 of DEGs didn't show any genetic similarities with known genes. DEGs were classified in eleven functional categories involving the abiotic stress response, biotic stress response, energy metabolism, cellular transport, catalitic activity, protein modification, amino acid metabolism and transcription factors. All the mutants were evaluated for their regulatory mechanisms against salt stress. The current data reveal that these six DEGs should be identified by next generation sequencing techniques and functional analysis should be design to understand the role of these six differentially expressed genes of tobacco mutants in further studies to improve new genetic resources.