Browsing by Author "Oktem, Huseyin Avni"

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DNA Aptamer-Based Colorimetric Detection Platform for Salmonella Enteritidis
(2017) Bayrac, Ceren; Eyidogan, Fusun; Oktem, Huseyin Avni; 28646719; ACA-9644-2022
Food safety is a major issue to protect public health and a key challenge is to find detection methods for identification of hazards in food. Food borne infections affects millions of people each year and among pathogens, Salmonella Enteritidis is most widely found bacteria causing food borne diseases. Therefore, simple, rapid, and specific detection methods are needed for food safety. In this study, we demonstrated the selection of DNA aptamers with high affinity and specificity against S. Enteritidis via Cell Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX) and development of sandwich type aptamer-based colorimetric platforms for its detection. Two highly specific aptamers, crn-1 and crn-2, were developed through 12 rounds of selection with K-d of 0.971 mu M and 0.309 mu M, respectively. Both aptamers were used to construct sandwich type capillary detection platforms. With the detection limit of 103 CFU/mL, crn-1 and crn-2 based platforms detected target bacteria specifically based on color change. This platform is also suitable for detection of S. Enteritidis in complex food matrix. Thus, this is the first to demonstrate use of Salmonella aptamers for development of the colorimetric aptamer-based detection platform in its identification and detection with naked eye in point-of-care.
Generating salt-tolerant Nicotiana tabacum and identification of stress-responsive miRNAs in transgenics
(2015) Aysin, Ferhunde; Erson-Bensan, Ayse Elif; Eyidogan, Fusun; Oktem, Huseyin Avni
Identification of vacuolar Na+/H+ antiporters facilitates the basis of salt stress tolerance mechanisms. Na+ accumulation into the vacuole is crucial for the avoidance of cytoplasmic Na+ toxicity. In this study, we show that the introduction of AtNHX1 into tobacco generated more tolerant plants when compared to wild-type plants. Transgenic tobacco plants exhibited higher germination rates in the presence of increasing salt concentrations compared to wild-type plants. In addition, proline levels were higher under salt stress conditions in both the shoots and the roots of transgenics compared to wild-type plants. Increase in malondialdehyde production during lipid peroxidation by salinity was lower in transgenic plants compared to the controls. Being important and newly discovered determiners of plant stress responses, microRNAs (miRNAs) are noncoding small RNAs and essential indicators of plant stress response mechanisms. For further identification of stress responses, the expression levels of growth and abiotic stress-related miRNAs (miR319a, miR319b, miR159b, miR398a, and miR398b) were quantified. miR319a, miR319b, and miR159b expression levels were higher in wildtype plants, and miR319a and miR159b expression was restored in transgenic plants. There was a slight decrease in the expression levels of miR398a and miR398b of wild-type plants. However, the recovery of the miR398a and miR398b expressions was especially significant in transgenic plants. Furthermore, an investigation of miRNAs in transgenic plants can help to understand the stress tolerance mechanisms of the plants.
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-9644-2022
In 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.
Target-Specific Delivery of Doxorubicin to Human Glioblastoma Cell Line Via Ssdna Aptamer
(2018) Bayrac, Abdullah Tahir; Akca, Oya Ercan; Eyidogan, Fusun Inci; Oktem, Huseyin Avni; 29485118; ACA-9644-2022
Targeted drug delivery approaches have been implementing significant therapeutic gain for cancer treatment since last decades. Aptamers are one of the mostly used and highly selective targeting agents for cancer cells. Herein, we address a nano-sized targeted drug delivery approach adorned with A-172 glioblastoma cell-line-specific single stranded DNA (ssDNA) aptamer in which the chemotherapeutic agent Doxorubicin (DOX) had been conjugated. DNA aptamer, GMT-3, was previously selected for specific recognition of glioblastoma and represented many advantageous characteristics for drug targeting purposes. Flow cytometry analysis proved the binding efficiency of the specific aptamer to tumour cell lines. Cell-type-specific toxicity of GMT-3:DOX complex was showed by XTT assay and terminated cytotoxic effects were screened for both target cell and a control breast cancer cell line. The result of this contribution demonstrated the potential utility of GMT-3 aptamer-mediated therapeutic drug transportation in the treatment of gliomas specifically. It was concluded that aptamer-mediated drug delivery can be applied successfully for clinical use.