Fakülteler / Faculties
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Item Retrieving Relevant Experiments: The Case of MicroRNA Microarrays(2015) Acici, Koray; Terzi, Yunus Kasim; Ogul, Hasan; 0000-0001-5612-9696; 0000-0002-3821-6419; 26116091; B-4372-2018; HDM-9910-2022Content-based retrieval of biological experiments in large public repositories is a recent challenge in computational biology and bioinformatics. The task is, in general, to search in a database using a query-by-example without any experimental meta-data annotation. Here, we consider a more specific problem that seeks a solution for retrieving relevant microRNA experiments from microarray repositories. A computational framework is proposed with this objective. The framework adapts a normal-uniform mixture model for identifying differentially expressed microRNAs in microanay profiling experiments. A rank-based thresholding scheme is offered to binarize real-valued experiment fingerprints based on differential expression. An effective similarity metric is introduced to compare categorical fingerprints, which in turn infers the relevance between two experiments. Two different views of experimental relevance are evaluated, one for disease association and another for embryonic germ layer, to discern the retrieval ability of the proposed model. To the best of our knowledge, the experiment retrieval task is investigated for the first time in the context of microRNA microarrays. (C) 2015 Elsevier Ireland Ltd. All rights reserved.Item Determination of Physiological, Biochemical and Molecular Interactions Between Fraser's Photinia (Photinia x fraseri Dress.) and Its Endophytic Bacterium PGB_invit(2022) Turkolmez, Nil; Karakaya, Merve; Ekinci, Muhammed Hamit; Lucas, Stuart James; Akkaya, Ozlem; Seker, Mine Gul; Kayihan, Ceyhun; Ciftci, Yelda OzdenAn endophytic beneficial bacterium was isolated and characterized from in vitro grown microshoots of Fraser's Photinia (Photinia x fraseri Dress.) in our previous studies. This bacterium, which is nominated as PGB_invit and determined as a member of Pseudorhodoplanes sp., has ability to fix nitrogen and produce plant growth promoting regulators such as indole acetic acid and gibberellic acid. Due to its beneficial traits, this specific bacterium promotes in vitro proliferation of Fraser's Photinia microshoots and enables microshoots to be conserved at 25 +/- 2oC for up to 16 months without requiring periodic subculture. Thus, the aim of the study is to identify physiological, biochemical and molecular influences of this bacterium together with determination of its localization in plant tissues. Our results showed that the optimum inoculum concentration of PGB_invit is 10(6) cfu ml(- 1) and the optimum incubation period is 60 days. Also, this study provides clear microscopic evidence of the endopyhtic bacterial colonization of GFP-labeled bacteria detected by confocal microscopy in Fraser's Photinia. Proline content was significantly enhanced in response to bacterial treatment whereas cellular H2O2 content was decreased. An increase in catalase activity was also detected, indicating that the results were consistent with the decrease in H2O2 content. Moreover, RNA sequencing (RNA-Seq) was also used to assess gene expression patterns and differential expression of five genes (predicted "MID1-Complementing Activity 1", Ubiquitin-conjugating enzyme E2, predicted "E3 ubiquitin-protein ligase RHA1B-like", 4-coumarate-CoA ligase-like 9, and methionine aminopeptidase 2B-like) between active and inactive form of the bacterium was confirmed by qRT-PCR. Among them, ubiquitin-conjugating enzyme E2 and predicted "E3 ubiquitin-protein ligase RHA1B-like genes which play important roles in plant immunity and stress were down-regulated in plant samples inoculated with bacteria which may demostrate that PGB_invit does not evoke plant immune system and has a positive effect on reducing stress on Fraser's Photinia. Key message PGB_invit (Pseudorhodoplanes sp.) has a positive impact on plants growth and development with several mechanisms. Besides its shown that PGB_invit is not act as a stress factor, as it does not cause a severe oxidative stress and thus can be used as a biofertilizer.Item Frequency of MCP-1 (rs1024611) and CCR2 (rs1799864) and Its Effect on Gene Expression Level in Patients with Agp(2017) Gunpinar, Sadiye; Alptekin, Nilgun Ozlem; Ucar, V. Betul; Acar, Hasan; 0000-0003-4104-6462; 28458180; G-1816-2014Objective: To identify the genetic risk markers of aggressive periodontitis (AgP), researchers focus on genetic components that regulate the immune response. Therefore the purpose of this study was to investigate genetic impact of monocyte chemoattractant protein (MCP)-1-2518 A/G and CC chemokine receptor 2 (CCR2) 190 G/A gene polymorphisms on AgP susceptibility and the effect of this polymorphism on MCP-1 gene expression in patients with AgP. Material and methods: A total of 215 subjects, 108 AgP and 107 periodontally healthy (H) were recruited in this cross-sectional study (NCT02817568). Gene polymorphisms of MCP -1-2518 A/G and CCR2-190 G/A were analyzed by a standard polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. MCP-1 messenger (m) RNA expression was measured using quantitative real-time (RT)-PCR in peripheral blood leukocytes from 26 AgP and 16 H controls. Threshold cycles (C-t) values were obtained from the RT-PCR analysis based on SYBR Green detection and data was normalized via triangle C-t. Results: There were no differences between AgP and H groups with regard to MCP-1 and CCR2 genotype distribution and allele frequencies (p > 0.05). In contrast, the MCP-1 mRNA expression levels were higher in homozygous "AA" control subjects than having G(+) genotype and AA homozygous AgP patients. Conclusions: It can be concluded that MCP-1 and CCR2 polymorphisms are not associated with AgP in Turkish population. Although in AgP patients, there was AA genotype with MCP -1 mRNA expression it can be speculated that gene expression levels in peripheral blood may not reflect the cytokine/chemokine levels of local tissues.Item Microrna Expression Prediction: Regression from Regulatory Elements(2016) Ogul, Hasan; Tuncer, M. EmreMicroRNAs are known as important actors in post-transcriptional regulation and relevant biological processes. Their expression levels do not only provide information about their own activities but also implicitly explain the behaviors of their targets, thus, in turn, the circuitry of underlying gene regulatory network. In this study, we consider the problem of estimating the expression of a newly discovered microRNA with known promoter sequence in a certain condition where the expression values of some known microRNAs are available. To this end, we offer a regression model to be learnt from the expression levels of other microRNAs obtained through a microarray experiment. To our knowledge, this is the first study that evaluates the predictability of microRNA expression from the regulatory elements found in its promoter sequence. The results obtained through the experiments on real microarray data justify the applicability of the framework in practice. (C) 2015 Nakcz Institute of Biocybemetics and Biomedical Engineering. Published by Elsevier Sp. z o.o. All rights reserved.Item Frequency of MCP-1 (Rs1024611) and CCR2 (Rs1799864) Gene Polymorphisms, and Its Effect on Gene Expression Level in Patients with Agp(2017) Gunpinar, Sadiye; Alptekin, Nilgun Ozlem; Ucar, V. Betul; Acar, Hasan; https://orcid.org/0000-0003-4104-6462; 28458180; G-1816-2014Objective: To identify the genetic risk markers of aggressive periodontitis (AgP), researchers focus on genetic components that regulate the immune response. Therefore the purpose of this study was to investigate genetic impact of monocyte chemoattractant protein (MCP)-1-2518 A/G and CC chemokine receptor 2 (CCR2) 190 G/A gene polymorphisms on AgP susceptibility and the effect of this polymorphism on MCP-1 gene expression in patients with AgP. Material and methods: A total of 215 subjects, 108 AgP and 107 periodontally healthy (H) were recruited in this cross-sectional study (NCT02817568). Gene polymorphisms of MCP -1-2518 A/G and CCR2-190 G/A were analyzed by a standard polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. MCP-1 messenger (m) RNA expression was measured using quantitative real-time (RT)-PCR in peripheral blood leukocytes from 26 AgP and 16 H controls. Threshold cycles (C-t) values were obtained from the RT-PCR analysis based on SYBR Green detection and data was normalized via triangle C-t. Results: There were no differences between AgP and H groups with regard to MCP-1 and CCR2 genotype distribution and allele frequencies (p > 0.05). In contrast, the MCP-1 mRNA expression levels were higher in homozygous "AA" control subjects than having G(+) genotype and AA homozygous AgP patients. Conclusions: It can be concluded that MCP-1 and CCR2 polymorphisms are not associated with AgP in Turkish population. Although in AgP patients, there was AA genotype with MCP -1 mRNA expression it can be speculated that gene expression levels in peripheral blood may not reflect the cytokine/chemokine levels of local tissues.Item Physiological, Biochemical, and Transcriptomic Responses to Boron Toxicity in Leaf and Root Tissues of Contrasting Wheat Cultivars(2017) Kayihan, Ceyhun; Oz, Mehmet Tufan; Eyidogan, Fusun; Yucel, Meral; Oktem, Huseyin Avni; ACA-9644-2022In this study, we examined physiological, biochemical, and transcriptomic responses to toxic boron (B) treatment in leaves and roots of two wheat cultivars in order to gain better insight into B response or tolerance mechanisms. Delayed development and reduced vigor caused by high B were not observed in leaves and roots of both cultivars. Length, wet weight, and dry weight were not markedly changed under B toxicity. In leaves, when compared to control, 995 and 892 genes were significantly expressed at least twofold under B toxicity in Atay and Bolal, respectively. In roots, expressions of 1248 and 957 genes were responsive to B toxicity in Atay and Bolal, respectively. In leaf and root tissues, B toxicity induced more genes related to protein degradation in Atay than those in Bolal. These differences in transcriptome were attributed to higher B accumulation in the sensitive cultivar which required high level of metabolic adjustment. B toxicity stress did not cause any significant change in photosynthetic activity and contents of proline and glycine betaine in both cultivars. Coordinately, we did not find any differentially expressed genes required for proline and glycine betaine metabolisms. Genes related to hormone signaling, kinases, transcription factors such as WRKY and MYB, and key enzymes in reactive oxygen species (ROS) scavenging mechanisms were differentially affected by B toxicity in both cultivars. Among commonly regulated genes in Atay and Bolal, glutathione S-transferase (GST) and NIP4;1 (nodulin-26-like intrinsic proteins) genes stand out as prominent actors in B stress response.Item Biological behaviors of muscarinic receptors in mesenchymal stem cells derived from human placenta and bone marrow(2020) Yegani, Arash Alizadeh; Maytalman, Erkan; Kozanoglu, Ilknur; Terzi, Menderes Yusuf; Aksu, Fazilet; 0000-0002-5268-1210; 32405354; AAE-1241-2021Objective(s): Cells perform their functional activities by communicating with each other through endogenous substances and receptors. Post-translation, stem cells function properly in new host tissue by carrying specific cell surface receptors. We aimed to characterize muscarinic receptor subtypes in mesenchymal stem cells (MSCs) together with osteogenic and adipogenic differentiation markers. Materials and Methods: mRNA levels of 5 muscarinic receptor subtypes (CHRM1 to 5), BMP-6, and PPAR gamma during osteogenic and adipogenic differentiation, under the effect of atropine blockade, were measured in MSCs obtained from human fetal membrane (FM) and bone marrow (BM). Additionally, the effect of atropine on differentiation in the 1st, 2nd, and 3rd passages of MSCs, obtained from human FM and BM, were analyzed by RT-qPCR. Results: CHRM1 mRNA levels increased in the FM group, while decreasing in the BM group. We found significant decreases in CHRM3 and CHRM5 mRNA levels in FM and BM groups, respectively. Atropine had variable effects based on cell source and receptor type. BMP-6 mRNA levels in differentiated osteogenic cells increased significantly compared to undifferentiated cells in both FM and BM groups. In MSCs derived from both sources, PPAR gamma mRNA levels in differentiated adipogenic cells increased significantly. Atropine showed no effect on MSCs differentiation. Conclusion: These results indicate that expressions of muscarinic receptors in MSCs derived from BM and FM can vary and these cells keep the potential of osteogenic and adipogenic differentiation in vitro. Besides, atropine had no effect on adipogenic and osteogenic differentiation of MSCs.Item Regulation of boron toxicity responses via glutathione-dependent detoxification pathways at biochemical and molecular levels in Arabidopsis thaliana(2019) Kayihan, Doga Selin; Kayihan, Ceyhun; Ciftci, Yelda Ozden; 0000-0002-9799-3648; Y-6244-2018The fine-tuned regulation of the Halliwell-Asada cycle (ascorbate-glutathione pathway) in Arabidopsis thaliana under boron (B) toxicity was shown in our previous report. In this study, we investigated the expression levels of some members of the glutathione S-transferase (GST) superfamily, such as phi (GSTF2, GSTF6, GSTF7, and GSTF8), tau (GSTU19), and zeta (GSTZ1) classes in Arabidopsis thaliana that were exposed to 1 mM boric acid (1B) and 3 mM boric acid (3B). Additionally, the expression levels of genes for glutathione (GSH) and phytochelatin biosynthesis as well as miR169 and miR156 were evaluated in Arabidopsis thaliana exposed to 1B and 3B. Moreover, changes in the levels of total GST activity; GSH; and total, protein-bound, and nonprotein thiols were spectrophotometrically determined. GSH levels and nonprotein thiol content did not change significantly following both B-toxicity conditions. Expression levels of GSH1 and GSH2 stayed stable under 1B toxicity; however, GSH1 expression increased significantly under 3B conditions in Arabidopsis thaliana. The expression levels of four genes from phi class members of GST were not dramatically changed under B-toxicity conditions. However, the transcript levels of miR169, ATGSTU19, and ATGSTZ1 were significantly increased after 1B and 3B exposure. These GST genes may have a role in the dramatic increase of total GST activity under toxic B. To the best of our knowledge, this is the first report displaying an integrative view of high-B-induced regulation of GSH-dependent enzymatic machinery at different biological organization levels in Arabidopsis thaliana.