Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
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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.Review A review on the removal of viruses by adsorption(Gazi University, 2023) Eren, Muhammet Şakir Abdullah; Tanaydın, Elif Sila; Arslanoğlu, Hasan; Çiftçi, HarunThe potential dangers of Covid-19 (SARS-CoV-2 Infection), which spread to almost all countries from Wuhan, China's Hubei province in 2020, have been the focus of attention of scientists worldwide Serious impact processes of Covid-19, ranging from pneumonia to severe acute respiratory infections and from kidney failure to death, continue to threaten millions of people. Isolation of pandemic species is of great importance for the development of appropriate treatment protocols in emerging viral infections. For this, it is necessary to develop existing methods as well as new methods. Viruses do not exist in living form in nature and they need other creatures to transfer their genetic material. In this respect, water resources and air appear as the most important means of transmission. Adsorption processes for the transmission means can be applied to prevent the spread of viruses and to inactivate them. In this review, the interactions of viruses with various adsorbents containing carbonaceous, oxidized, porous anf metal organic framework materials were examined. Electrostatic interactions were found to be more effective in target types of adsorbing processes of adsorbents used in water and air purification. Since the virus surface carries various organic functional groups, it is seen that it will interact with different adsorbents electrostatic and in this way they can be removed and both isolated and rendered ineffective. We think that our study will contribute to effective solutions to prevent the spread of other pathogens, including coronaviruses, by adsorption processes to be applied to air and water sources and to disinfect the specified transmission means.Article Epithelial-Mesenchymal Transition as a Potential Route for Dapt Resistance in Breast Cancer Cells(Walter de Gruyter GmbH, 2023) Tellı, Kubra; Ozuysal, Ozden Yalcın; Telli, Kübra; Yalçın Özuysal, ÖzdenObjectives: Notch is a conserved pathway involved in cell- fate determination and homeostasis. Its dysregulation plays a role in poor prognosis and drug resistance in breast cancer. Targeting Notch signaling via inhibition of the gamma- secretase complex is in the spotlight of modern cancer treat- ments. Gamma-secretase inhibitors (GSI) have shown suc- cessful clinical activity in treating cancers, yet the possible resistance mechanism remains unstudied. Modeling the resistance and understanding culprit molecular mechanisms can improve GSI therapies. Accordingly, the aim of this study is to generate and analyze GSI-resistant breast cancer cells. Methods: Gradually increasing doses of DAPT, a well-known GSI, were applied to MCF-7 breast cancer cell lines to generate resistance. Cell viability, migration and gene expressions were assessed by MTT, wound healing and qRT-PCR analyses. Results: DAPT-resistant MCF-7 cells exhibited abnormal expression of Notch receptors, Notch targets (HES1, HES5, HEY1), and epithelial-mesenchymal transition (EMT) markers (E-cadherin, ZO-1, SNAIL2, N-cadherin) to overcome the continuous increase in DAPT toxicity by increased migration through mesenchymal transition. Conclusions: This study prospects into the role of EMT in the potential resistance mechanism against DAPT treatment for breast cancer cells. Complementary targeting of EMT should be investigated further for a possible effect to potentiate DAPT’s anti-cancer effects.Article Citation - WoS: 4Citation - Scopus: 4Protocol for Cell Surface Biotinylation of Magnetic Labeled and Captured Human Peripheral Blood Mononuclear Cells(Elsevier, 2022) Ayaz Güner, Şerife; Acar, Mustafa Burak; Boyvat, Dudu; Güner, Hüseyin; Bozalan, Habibe; Güzel, Melis; Yıldır, Selin Kübra; Altınsoy, Nilay; Fındık, Fatma; Karakükçü, Musa; Özcan, ServetAnalysis of the surfaceome of a blood cell subset requires cell sorting, followed by surface protein enrichment. Here, we present a protocol combining magnetically activated cell sorting (MACS) and surface biotinylation of the target cell subset from human peripheral blood mononuclear cells (PBMCs). We describe the steps for isolating target cells and their in-column surface biotinylation, followed by isolation and mass spectrometry analysis of biotinylated proteins. The protocol enables in-column surface biotinylation of specific cell subsets with minimal membrane disruption.Article Adsorpsiyon ile Virüslerin Giderilmesine İlişkin Bir İnceleme(Gazi Üniversitesi, 2021) Eren, Muhammet Şakir Abdullah; Tanaydın, Elif Sıla; Arslanoğlu, Hasan; Çiftçi, Harun2020 yılında Çin’in Hubei eyaletinin Vuhan şehrinden neredeyse tüm ülkelere yayılan Covid-19 (SARS-CoV-2 Enfeksiyonu)’un potansiyel tehlikeleri, dünya çapında bilim insanlarının ilgi odağı olmuştur. Covid-19’un pnömoniden ağır akut solunum yolu enfeksiyonlarına ve böbrek yetmezliğinden ölüme kadar uzanan ciddi etki süreçleri milyonlarca insan için tehdidini sürdürmektedir. Ortaya çıkan yeni viral enfeksiyonlarda uygun tedavi protokollerinin geliştirilmesi için pandemik türlerin izolasyonu büyük önem arz etmektedir. Bunun için yeni yöntemlerin yanında mevcut yöntemlerin de geliştirilmesi gereklidir. Virüsler doğada canlı formda bulunmazlar ve genetik materyalini aktarabilmek için başka canlılara ihtiyaç duyarlar. Ayrıca izole edilmiş yüzeylerde hızla inaktif hale getirilebilirler. Bu yönüyle su kaynakları ve hava en önemli iletim vasıtaları olarak karşımıza çıkmaktadır. Virüslerin yayılmasının önüne geçmede ve onları etkisiz hale getirmede iletim vasıtalarına yönelik adsorpsiyon işlemleri uygulanabilmektedir. Bu derlemede, virüslerin karbonlu, oksitli, gözenekli materyaller ve metal organik kafes yapıları içeren çeşitli adsorbanlarla etkileşimleri incelendi. Su ve hava arıtmasında kullanılan adsorbanların hedef türleri adsorplama işlemlerinde elektrostatik etkileşimlerin daha etkili olduğu belirlendi. Virüs yüzeyinin çeşitli organik fonksiyonel grupları taşıması nedeniyle farklı adsorbanlar ile elektrostatik etkileşime geçeceği ve bu şekilde de onların uzaklaştırılarak hem izole edilmesi hem de etkisiz hale getirilmesi mümkün görülmektedir. Çalışmamızın Koronavirüsler dahil diğer patojenlerin hava ve su kaynaklarına uygulanacak adsorpsiyon işlemleri ile yayılmalarının engellenmesine ve belirtilen iletim vasıtalarının dezenfekte edilmesine yönelik etkili çözümlere katkı sağlayacağını düşünmekteyiz.Article Citation - WoS: 1Pasif Tümör Hedefli İnorganik İlaç Nanotaşıyıcıların Akciğer Sağlıklı ve Kanser Hücreleri Üzerindeki Uzun Dönemli Etkisi(Gazi Üniversitesi, 2020) Dağlıoğlu, Cenk; Kacı, Fatma Necmiyeİlaç nanotaşıyıcıları, kontrollü ve sürekli ilaç salım özellikleri ile kanser tedavisinde büyük bir potansiyele sahiptir. Bu nanotaşıyıcılar pasif veya aktif hedefli olarak ilaç taşınımı sağlayabilmektedir, ancak aktif hedefli muadillerine göre, pasif hedefli nanotaşıyıcılar tümörlü dokularda daha yavaş ve düşük düzeyde ilaç birikimi sağladığından kanserli hücrelerin yanında sağlıklı hücrelerde uzun süre bu nanotaşıyıcılara maruz kalmaktadır. Bu nedenle, bu çalışmada, pasif hedefli ilaç nanotaşıyıcıların insan akciğer epitel BEAS-2B hücreleri ve insan akciğer kanser A549 hücreleri üzerindeki uzun dönem etkileri araştırıldı. Bunun için, görüntüleme ve tedavi edici özellikleri bir arada barından Fe3O4@SiO2(FITC)-DOX formülasyonuna sahip ilaç nanotaşıyıcıları kullanıldı ve hücresel birikim, sitotoksisite ve apoptoz üzerindeki etkileri araştırıldı. Hücresel alım ve sitotoksisite deneyleri, pasif hedefli nanotaşıyıcıların kanser hücresi canlılığının etkin bir şekilde azalttığını gösterirken, 24 saatlik inkübasyon sürecinde sağlıklı hücreler üzerinde kayda değer bir etki görülmedi. Ancak 96 saatlik uzun inkübasyon sürecinde, sağlıklı BEAS-2B hücreleri makul seviyelerde nanotaşıyıcı alımı gerçekleştirirken, A549 kanser hücrelerine kıyasla düşük düzeylerde ilaç-aracılı sitotoksisite sergiledi. Ayrıca, nanotaşıyıcılar A549 hücrelerindeki apoptoz seviyelerini önemli ölçüde artırırken, BEAS-2B hücrelerinde 96 saat sonunda dahi apoptotik etki göstermedi. Bu sonuçlar, pasif hedefli inorganik ilaç nanotaşıyıcıların, sağlıklı hücreleri ihmal edilebilir düzeyde etkileyerek, antikanser ilaçların kemoterapötik etkilerini artırmada umut verici olduğunu göstermektedir.Article Citation - WoS: 2Citation - Scopus: 2Antiviral Microrna Expression Signatures Are Altered in Subacute Sclerosing Panencephalitis(Wolters Kluwer Medknow Publications, 2021) Tüfekçi, Kemal Uğur; Allmer, Jens; Çarman, Kürşat Bora; Bayram, Erhan; Topçu, Yasemin; Hız, Semra; Genç, Şermin; Yiş, UluçBackground: Subacute sclerosing panencephalitis (SSPE) is a chronic, progressive disease caused by a persistent infection of the measles virus. Despite extensive efforts, the exact neurodegeneration mechanism in SSPE remains unknown. MicroRNAs (miRNAs) have emerged as an essential part of cellular antiviral defense mechanisms and can be modulated by antiviral cytokines Such as interferon-beta (IFN-beta). Aims and Objectives: In this study, we aimed to elucidate the role of antiviral miRNAs in the pathogenesis of SSPE and analyze the interaction between host antiviral miRNAs and virus genes. Materials and Methods: Thirty-seven patients who were followed with SSPE and age-matched healthy children were included in the study. Peripheral blood mononuclear cell levels of miR-196b, miR-296, miR-431, and miR-448 were analyzed using quantitative polymerase chain reaction. Target predictions and pathway constructions of deregulated miRNAs were assessed. Results: Here, we showed that IFN-beta-modulated miR-196b, miR-296, and miR-431 were significantly upregulated in patients with SSPE compared with healthy controls. Besides, sequence complementarity analysis showed that miR-296 and miR-196b predicted binding regions in measles virus genomic RNA. Conclusion: Our findings suggest that antiviral miRNAs are upregulated in patients with SSPE, which could be a part of the host antiviral defense mechanism. </p>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.Article Citation - WoS: 8Citation - Scopus: 8Simple High-Performance Liquid Chromatographic Method for Determination of Donepezil Hcl in Pharmaceutical Formulations(ACG Publications, 2020) Bulduk, İbrahim; Aydın, Beyza SultanDonepezil HCl is a hydrochloride salt of a piperidine derivative acetylcholinesterase inhibitor and, it uses in treatment demantia of Alzheimer’s disease. In this study, a sensitive and rapid HPLC-UV method was developed and validated for determination of Donepezil HCl in API and tablet dosage forms. Chromatographic separation was performed using a Ace 5 C18 (5 ?m, 250 x 4.6 mm) by using isocratic phosphate buffer at pH:2.0 and acetonitrile (55:45, v/v) mobile phase was used at the rate of 1.2 mL/min. The column temperature was set at 30 ?C and the UV detection was recorded at 268 nm. The method was validated with respect to specificity, precision, accuracy, linearity, repeatability and reproducibility parameters in a concentration range of 25-125 µg/mL. The limit of detection (LOD) and limit of quantification (LOQ) were determined as 1.40 and4.20 µg/mL, respectively. The uncertainty budget of the measurement for Donepezil HCl was estiamted as 5.80 % at 95% confidence level (k = 2).