Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Blank Frame and Intensity Variation Distortion Detection and Restoration Pipeline for Phase-Contrast Microscopy Time-Lapse Images(Aves, 2024) Ucar, Mahmut; Iheme, Leonardo O.; Onal, Sevgi; Pesen-Okvur, Devrim; Yalcin-Ozuysal, Ozden; Toreyin, Behcet U.; Unay, DevrimIn this study, we propose a preprocessing pipeline for the detection and correction of distorted frames in time-lapse images obtained from phase-contrast microscopy. The proposed pipeline employs the average intensities of frames as a foundational element for the analysis. In order to evaluate the degree of correction required for intensity variance, a normalization technique is applied to the difference between the average intensity of a specific frame and the median average intensity of all frames within the study. Our restoration method increases the histogram similarity between the distorted and non-distorted frames, preserves trans-passing pixels in regions of interest, and mitigates the development of additional distortions. The efficacy of the proposed method was evaluated using 15 395 time-lapse image frames from 27 experiments using our own dataset and 830 time-lapse images from four different experiments obtained from the cell tracking challenge. The results of the validation demonstrate a high degree of numerical and visual accuracy of the proposed pipeline.Article Citation - WoS: 15Citation - Scopus: 16The Usability of Juniperus Virginiana L. as a Biomonitor of Heavy Metal Pollution in Bishkek City, Kyrgyzstan(Taylor & Francis, 2015) Kurmanbekova, Gülbübü; Severoğlu, Zeki; Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yalçın, İbrahim Ertuğrul; Kaşoğlu, GültenUncontrolled and unplanned urbanization and industrialization due to increase of population and rapid industrial development have created severe environmental problems in Kyrgyzstan during the last few decades. In this study, Juniperus virginiana, a dioecious species, was employed in order to make assessment of the heavy metal pollution rate in the area and of the heavy metal pollution impact on the mineral nutrient status of the plant. For this study, leaf (washed and unwashed) and bark samples of J. virginiana, and its co-located soil samples were collected from eight different stations, all in the capital of Kyrgyzstan, Bishkek, in 2012 vegetation period. The standard procedures were used and the determinations of heavy metal and nutrient element contents (Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Pb and Zn) in all samples were done using inductively coupled plasma-optical emission spectroscopy. According to our measurements, J. virginiana was found to be capable of accumulating a considerable amount of metals and the mineral nutrient uptake pattern was altered because of metal deposition in the plant, which showed a contamination risk in the area.Article Citation - WoS: 20Citation - Scopus: 19Using the Turkish Red Pine Tree To Monitor Heavy Metal Pollution(HARD, 2020) Yalçın, Ertuğrul; Özyiğit, İbrahim İlker; Doğan, İlhan; Demir, Göksel; Yarcı, CelalTurkish red pine is an evergreen tree species widely distributed in the Aegean and Mediterranean regions in Turkey. In the present work, the heavy metal pollution level in Istanbul was investigated using Turkish red pine as a biomonitor. For determining heavy metal concentrations (Cd, Co, Cr, Mn, Ni and Pb) in leaf (unwashed and washed) and bark samples of Turkish red pine and its co-located soil samples we used ICP-OES. Additionally, particulate matter profiles of the research areas were investigated. The samples were collected from 5 different localities: 4 from the Bosporus region (Yildiz Grove, Fethi Pasha Grove, Baltalimani Grove and Mihrabad Grove) and one from Prince Island, also known as Buyukada (as control). According to our measurements, the highest heavy metal accumulations (in mg kg(-1) DW) in plant part samples were measured between 1.526 +/- 0.012 and 1.639 +/- 0.015 for Cd, 0.543 +/- 0.007 and 0.600 +/- 0.009 for Co, 5.110 +/- 0.064 and 5.648 +/- 0.072 for Cr, 9.347 +/- 0.105 and 10.331 +/- 0.111 for Mn, 7.483 +/- 0.091 and 8.271 +/- 0.096 for Ni, and 13.848 +/- 0.159 and 14.950 +/- 0.167 for Pb, while the highest heavy metal accumulations (in mg kg(-1) DW) in soil samples were measured between 1.813 +/- 0.021 and 1.974 +/- 0.029 for Cd, 6.326 +/- 0.082 and 6.992 +/- 0.091 for Co, 22.017 +/- 0.284 and 23.685 +/- 0.301 for Cr, 268.333 +/- 3.153 and 297.361 +/- 3.529 for Mn, 15.194 +/- 0.176 and 16.792 +/- 0.193 for Ni, and 68.778 +/- 0.715 and 74.514 +/- 0.883 for Pb. The highest outdoor particulate matter levels (in mu g/m(3)) in research areas were also determined as 27.103 for fine (PM2.5) and 67.792 for coarse (PM10) aerosols. The findings revealed that Turkish red pine could accumulate noteworthy amounts of heavy metals.Conference Object Effects of Hesperidin on Non-Small Cell Lung Cancer Cells(International Institute of Anticancer Research, 2014) Bireller, Elif Sinem; Cincin, Zeynep Birsu; Ünlü, Miray; Kıran, Bayram; Baran, Yusuf; Çakmakoğlu, BediaBackground: Hesperidin, a glycoside flavonoid that is found in citrus fruits, and the mechanisms of hesperidin-induced apoptosis are not well understood. In this study, we aimed to investigate the cytotoxic and apoptotic aspect of hesperidin induction in lung cancer.Article Citation - WoS: 6Citation - Scopus: 9Detection of Physiological and Genotoxic Damages Reflecting Toxicity in Kalanchoe Clones(Global Network Environmental Science & Technology, 2016) Özyiğit, İbrahim İlker; Yılmaz, S.; Doğan, İlhan; Sakçalı, Mehmet Serdal; Tombuloğlu, Güzin; Demir, GökselIn order to make assessments in understanding of physiological and genotoxic effects of imposing cadmium (Cd) on photosynthetic pigment contents along with the changes occurring in genetic material of Kalanchoe plants were used in relation to various Cd-treatments. Young plantlets were originated from a single host plant as clones, and developed in vitro. Developed clones were grown in standard pots with daily watering of Hoagland solution (20 ml) containing different concentrations of cadmium chloride for two months. Cd concentrations of the collected samples were measured by employing ICP-OES and RAPD-PCR technique was applied for detecting the genotoxic effects of Cd. After two month of experimental period, the comparisons between unexposed and exposed Kalanchoe clone groups revealed reductions in photosynthetic pigment contents, especially at the highest level of Cd exposure and a genomic instability when application of Cd concentration increases. RAPD-PCR analyses demonstrated the distinguishable banding pattern in number and band intensities between Cd-treated and control groups. In addition, progressive Cd accumulations in leaves, stems and roots of plant samples were observed when the application of exposure level increased.Article Citation - WoS: 16Citation - Scopus: 16Screening of Damage Induced by Lead (pb) in Rye (secale Cereale L.) – a Genetic and Physiological Approach(Taylor and Francis Ltd., 2016) Özyigit, İbrahim İlker; Doğan, İlhan; İğdelioğlu, Sezen; Filiz, Ertuğrul; Karadeniz, Sedat; Uzunova, ZeynepThe fields in which lead (Pb) finds application in the modern world have increased dramatically in recent years. As a consequence of this intensive utilization of Pb, its toxicity tends to pose more and more environmental problems. The aim of this study was to evaluate the genotoxic potential of Pb and to characterize some physiological parameters in Secale cereale under Pb stress. Plants were subjected to different exposure levels of Pb (0, 100, 200 and 400 µmol/L) for two weeks. At the end of the experimental period, the effects of Pb exposure on the photosynthetic pigments content (chlorophyll a and b, total chlorophyll, chlorophyll a/b and carotenoids) and genetic material of S. cereale were studied. To evaluate the genotoxic effect of Pb, random amplified polymorphic DNA – polymerase chain reaction (RAPD-PCR) was employed. The obtained results showed alteration in the photosynthetic pigments content and RAPD-PCR profiles of S. cereale grown in the presence of Pb. The alterations in the RAPD-PCR profiles following Pb treatments appeared to be losses of normal bands and occurrences of new bands compared to unexposed plantlets. Overall, the content of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids decreased by 6.68%, 6.08%, 2.89% and 8.57%, respectively, under severe Pb stress (400 µmol/L).Article Citation - WoS: 18Citation - Scopus: 20Assessment of Cd-Induced Genotoxic Damage in Urtica Pilulifera L. Using Rapd-Pcr Analysis(Taylor and Francis Ltd., 2016) Doğan, İlhan; Özyiğit, İbrahim İlker; Tombuloğlu, Güzin; Sakçalı, Mehmet Serdal; Tombuloğlu, HüseyinPlants can be used as biological indicators in assessing the damage done by bioaccumulation of heavy metals and their negative impact on the environment. In the present research, Roman nettle (Urtica pilulifera L.) was employed as a bioindicator for cadmium (Cd) pollution. The comparisons between unexposed and exposed plant samples revealed inhibition of the root growth (∼25.96% and ∼45.92% after treatment with 100 and 200 µmol/L Cd concentrations, respectively), reduction in the total soluble protein quantities (∼53.92% and ∼66.29% after treatment with 100 and 200 µmol/L Cd concentrations, respectively) and a gradual genomic instability when the Cd concentrations were increased. The results indicated that alterations in randomly amplified polymorphic DNA (RAPD) profiles, following the Cd treatments, included normal band losses and emergence of new bands, when compared to the controls. Also, the obtained data from F1 plants, utilized for analysis of genotoxicity, revealed that DNA alterations, occurring in parent plants due to Cd pollution, were transmitted to the next generation.Article Citation - WoS: 12Citation - Scopus: 17Pyramiding Multiple Genes for Resistance To Pvy, Tswv and Pmmov in Pepper Using Molecular Markers(Verlag Eugen Ulmer, 2014) Özkaynak, E.; Devran, Z.; Kahveci, E.; Doğanlar, Sami; Başköylü, B.; Doğan, F.; İşleyen, M.; Yüksel, A.; Yüksel, M.Pepper (Capsicum annuum L.) is one of the most important vegetables cultivated worldwide. Many pests and pathogens cause economic yield losses in pepper. Potato virus Y (PVY), Tomato spotted wilt virus (TSWV) and Pepper mild mottle virus (PMMoV) are considered among the most destructive viruses affecting pepper in the world. Because chemical treatments have limited success for managing PVY, TSWV and PMMoV, resistant varieties are considered to be the most effective means of controlling these viruses. In this study, resistance genes to these viruses were successfully transferred to the superior sweet Charleston pepper line 'Y-CAR' using molecular markers and biological assays. As a result, a new line which is resistant to PVY, TSWV and PMMoV was developed. The results also showed the applicability of a pyramiding strategy for breeding multiple virus resistance in pepper. © Verlag Eugen Ulmer KG, Stuttgart.Article Citation - WoS: 20Apoptotic Effects of Resveratrol, a Grape Polyphenol, on Imatinib-Sensitive and Resistant K562 Chronic Myeloid Leukemia Cells(International Institute of Anticancer Research, 2012) Can, Geylani; Çakır, Zeynep; Kartal, Melis; Gündüz, Ufuk; Baran, YusufTo examine the antiproliferative and apoptotic effects of resveratrol on imatinib-sensitive and imatinib-resistant K562 chronic myeloid leukemia cells. Antiproliferative effects of resveratrol were determined by the 3-Bis[2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5-carboxanilide inner salt (XTT) cell proliferation assay. Apoptotic effects of resveratrol on sensitive K562 and resistant K562/IMA-3 cells were determined through changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP), and apoptosis by annexin V-(FITC). The concentrations of resveratrol that inhibited cell growth by 50% (IC(50)) were calculated as 85 and 122 μM for K562 and K562/IMA-3 cells, respectively. There were 1.91-, 7.42- and 14.73-fold increases in loss of MMP in K562 cells treated with 10, 50, and 100 μM resveratrol, respectively. The same concentrations of resveratrol resulted in 2.21-, 3.30- and 7.65-fold increases in loss of MMP in K562/IMA-3 cells. Caspase-3 activity increased 1.04-, 2.77- and 4.8-fold in K562 and 1.02-, 1.41- and 3.46-fold in K562/IMA-3 cells in response to the same concentrations of resveratrol, respectively. Apoptosis was induced in 58.7%- and 43.3% of K562 and K562/IMA-3 cells, respectively, in response to 100 μM resveratrol. Taken together these results may suggest potential use of resveratrol in CML, as well as in patients with primary and/or acquired resistance to imatinib.Article Citation - WoS: 10Citation - Scopus: 14Enalapril-Induced Apoptosis of Acute Promyelocytic Leukaemia Cells Involves Stat5a(International Institute of Anticancer Research, 2012) Purçlutepe, Özlem; İskender, Güniz; Kiper, Hatice Demet; Tezcanlı, Burçin; Selvi, Nur; Biray Avcı, Çığır; Kosova, Buket; Adan Gökbulut, Aysun; Şahin, Fahri; Baran, Yusuf; Saydam, GürayBackground: In this study, we aimed at evaluating the cytotoxic and apoptotic effects of enalapril on human HL60 acute promyelocytic leukaemia cells and at clarifying the roles of signal transducers and activator of transcription proteins (STATs) on enalapril-induced cell death. Materials and Methods: Cell viability and cytotoxicity tests were conducted by Trypan blue dye exclusion and 2,3-Bis[2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5- carboxanilide inner salt (XTT) assays, respectively. Apoptotic analyses were performed by the AnnexinV-enhanced green fluorescent protein (EGFP) staining method and by fluorescence microscopy. Expression levels of STAT3, -5A and -5B genes were analysed by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). Results: The results showed that enalapril reduced viability and proliferation, and induced apoptosis in HL60 cells in a dose-and time-dependent manner as compared to untreated controls. The expression levels of STAT5A gene were significantly reduced in enalapril-treated HL60 cells as compared to untreated controls. Conclusion: Taken together, all data showed for the first time that enalapril has significant anticancer potential for the treatment of acute premyelocytic leukaemia.