Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Conference Object Citation - Scopus: 2Yara İyileşmesi Mikroskopi Görüntü Serilerinin Otomatik Analizi - Bir Ön-çalışma(IEEE, 2020) Mayalı, Berkay; Şaylığ, Orkun; Pesen Okvur, Devrim; Yalçın Özuysal, Özden; Töreyin, Behçet Uğur; Ünay, Devrim; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyCollective cell analysis from microscopy image series is important for wound healing research. Computer-based automation of such analyses may help in rapid acquisition of reliable and reproducible results. In this study phase -contrast optical microscopy image series of an in-vitro wound healing essay is manually delineated by two experts and its analysis is realized, traditional image processing and deep learning based approaches for automated segmentation of wound area are developed and their perlOrmance comparisons are carried out.Conference Object Citation - Scopus: 1A Preliminary Study on Cell Motility Analysis From Phase-Contrast Microscopy Image Series(IEEE, 2020) Kayan, Emre; Pesen Okvur, Devrim; Önal, Sevgi; Pesen Okvur, Devrim; Yalçın Özuysal, Özden; Töreyin, Behçet Uğur; Ünay, Devrim; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyAnalyses of morphology, polarity, and motility of cells is important for cell biology research such as metastatic and invasive capacity of cells, wound healing, and embryonic development. Automation of such analyses using image series of phase-contrast optical microscopy, which allows label-free imaging of live cells in their living environment, is a need. With this purpose, in this study image series of a cell motility experiment is manually annotated, and an automation algorithm realizing motion and shape analyses of cells using the annotated data is developed. In addition, due to the low number of annotated data at hand, a U-Net based solution is devised for automated segmentation of the cells and its performance is evaluated.Article Citation - WoS: 1Citation - Scopus: 1The Current Status of Thrips Parasitoids Ceranisus (hymenoptera: Eulophidae) Species in Turkey Based on Morphology and 28s D2 Rdna(Türkiye Entomoloji Derneği, 2010) Doğanlar, Oğuzhan; Frary, Anne; Doğanlar, Mikdat; Frary, Anne; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyThe aim of this study was to investigate genetic analysis of the species within genus Ceranisus (Hymenoptera: Eulophidae) that are interesting groups found in South Eastern Anatolia and Eastern parts of Mediterranean Region of Turkey and to compare with the other thrips-parasitoids between May 2006 and May 2007. Totally, 143 specimens (30 male: 113 female) belonging to Ceranisus genus were collected from 20 locations of 38 different localities in Hatay, Gaziantep, Adiyaman and Sanliurfa provinces. The population was divided into 13 groups based on morphologic characters. Phylogenetic relationships amongst Ceranisus species (Chalcidoidea: Eulophidae) were gathered from DNA sequence data. Fifteen species of thrips chalcid parasitoids were analyzed using one gene, D2 domain of the 28S ribosomal DNA. Among morphologically distinct 13 species/taxonomic groups, 3 of them identified as new species according to the genetical analysis. Four of the other species occurred in C. nr. lepidotus group while 5 of C. nr. bozovaensis consisted of two groups. To conclude 3 new species of Ceranisus and 3 different groups that may yield new species were determined in Turkish Ceranisus population.Article Citation - WoS: 42Citation - Scopus: 48The Roles of Bioactive Sphingolipids in Resveratrol-Induced Apoptosis in Hl60 Acute Myeloid Leukemia Cells(Springer Verlag, 2011) Çakır, Zeynep; Saydam, Güray; Baran, Yusuf; Baran, Yusuf; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyPurpose Acute promyelocytic leukemia results from a translocation between 15 and 17 chromosomes that produce PML/RARa fusion protein. PML/RARa inhibits differentiation of myeloid precursor cells at stem cell level. Resveratrol is a phytoalexin that exerts cytotoxic effects on cancer cells. Ceramides have crucial roles in cell growth, proliferation, differentiation, drug resistance, and apoptosis. In this study, we examined the possible cytotoxic effects of resveratrol on acute myeloid leukemia cells and determined the roles of ceramide-metabolizing genes in resveratrol-induced apoptosis, in addition to investigating the possibility of increasing the sensitivity of HL60 cells to resveratrol by manipulating sphingolipids. Methods Cytotoxic effects of resveratrol, C8:ceramide, PDMP, and SK-1 inhibitor were determined by XTT cell proliferation assay. Changes in caspase-3 enzyme activity and mitochondrial membrane potential (MMP) were measured using caspase-3 colorimetric assay and JC-1 MMP detection kit. Expression levels of ceramide-metabolizing genes were examined by RT-PCR. Results The results revealed that manipulations of ceramide metabolism toward generation or accumulation of apoptotic ceramides increased apoptotic effects of resveratrol in HL60 cells, synergistically. More importantly, gene expression analyses revealed that resveratrol-induced apoptosis via increasing expression levels of ceramide generating genes and decreasing expression levels of antiapoptotic sphingosine kinase-1 and glucosylceramide synthase genes. Conclusion These results showed for the first time that increasing intracellular levels of ceramides by biochemical approaches has also increased sensitivity of HL60 cells to resveratrol. We also showed that resveratrol induces apoptosis through manipulating ceramide-metabolizing genes that resulted in the accumulation of ceramides in HL60 cells.