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Yayın Culturing, Freezing, Processing, and Imaging of Entire Organoids and Spheroids While Still in a Hydrogel(Journal of Visualized Experiments, 2022) Tok, Olgu Enis; Demirel, Gamze; Saatci, Yusuf; Akbulut, Zeynep; Kayalar, Özgecan; Aktas, Ranan GülhanOrganoids and spheroids, three-dimensional growing structures in cell culture labs, are becoming increasingly recognized as superior models compared to two-dimensional culture models, since they mimic the human body better and have advantages over animal studies. However, these studies commonly face problems with reproducibility and consistency. During the long experimental processes -with transfers of organoids and spheroids between different cell culture vessels, pipetting, and centrifuging -these susceptible and fragile 3D growing structures are often damaged or lost. Ultimately, the results are significantly affected, since the 3D structures cannot maintain the same characteristics and quality. The methods described here minimize these stressful steps and ensure a safe and consistent environment for organoids and spheroids throughout the processing sequence while they are still in a hydrogel in a multipurpose device. The researchers can grow, freeze, thaw, process, stain, label, and then examine the structure of organoids or spheroids under various high-tech instruments, from confocal to electron microscopes, using a single multipurpose device. This technology improves the studies' reproducibility, reliability, and validity, while maintaining a stable and protective environment for the 3D growing structures during processing. In addition, eliminating stressful steps minimizes handling errors, reduces time taken, and decreases the risk of contamination.Yayın The Effects of Glutathione on Clinically Essential Fertility Parameters in a Bleomycin Etoposide Cisplatin Chemotherapy Model(Mdpi, 2023) Bayram, Hale; Dönmez Çakıl, Yaprak; Sitar, Mustafa Erinc; Demirel, Gamze; Selam, Belgin; Cincik, MehmetChemotherapeutic agents used in the treatment of testicular cancer cause damage to healthy tissues, including the testis. We investigated the effects of glutathione on sperm DNA integrity and testicular histomorphology in bleomycin etoposide cisplatin (BEP) treated rats. Twelve-week-old male rats of reproductive age (n = 24) were randomly divided into three groups, the (i) control group, (ii) BEP group, and (iii) BEP+ glutathione group. Weight gain increase and testes indices of the control group were found to be higher than that of the BEP group and BEP+ glutathione group. While the BEP treatment increased sperm DNA fragmentation and morphological abnormalities when compared to the control group, GSH treatment resulted in a marked decrease for both parameters. Moreover, BEP treatment significantly decreased serum testosterone levels and sperm counts in comparison to the control group, yet this reduction was recovered in the BEP+ glutathione treated group. Similarly, seminiferous tubule epithelial thicknesses and Johnsen scores in testicles were higher in the control and BEP+ glutathione groups than in the BEP-treated group. In conclusion, exogenous glutathione might prevent the deterioration of male reproductive functions by alleviating the detrimental effects of BEP treatment on sperm quality and testicular histomorphology.Yayın The effects of low-dose sorafenib on epithelial-mesenchymal transition and multidrug resistance markers in HepG2 cell line(Prusa Medical Publishing, 2023) Dönmez Çakıl, Yaprak; Akbulut, Zeynep; Demirel, Gamze; Güneş Özünal, Zeynep; Aktaş, Gülhan RananObjectives: Sorafenib is an orally administered tyrosine kinase inhibitor in hepatocellular cancer. Low sorafenib concentrations are attained during pharmacotherapy due to pharmacokinetic profile and patient inadherence. Resistance to treatment is a limitation to improving survival. Underlying mechanisms include epithelial-mesenchymal transition. The aim of the study was to evaluate epithelial-mesenchymal transition and multidrug resistance-related parameters in HepG2 cells following low-dose and short-term sorafenib treatment. Methods: Epithelial-mesenchymal transition and multidrug resistance-related markers were examined by quantitative PCR, flow cytometry, and confocal laser scanning microscopy. Results: An increase in epithelial marker E-cadherin and downregulation of mesenchymal markers Vimentin and Snail1 were detected by gene expression analysis. While P-glycoprotein expression increased, multidrug resistance protein 1, and breast cancer resistance protein mRNA levels did not alter after sorafenib treatment. The accumulation of the ABC transporter substrate rhodamine 123 in the cells increased following the treatment, corresponding to a less efficient efflux of rhodamine 123 and a possible effect on other transporters and mechanisms. Conclusions: The results indicate a protective effect of sorafenib against epithelial-mesenchymal transition and upregulation in P-glycoprotein expression, which is, however, not sufficient to cause less intracellular rhodamine 123 accumulation. The effects of low-dose and short-term sorafenib on epithelial-mesenchymal transition and multidrug resistance-related markers might contribute to enlightening new treatment strategies in hepatocellular cancer.Yayın Karaciğer hücreleri ve organoidlerin üç boyutlu kültürlerinde kullanılmak üzere geliştirilmiş biyomalzemeler(2021) Demirel, GamzeDoku mühendisliği ve biyomühendislik çalışmaları başta olmak üzere biyoloji ve kimya gibi temel bilimlerin son zamanlarda üzerinde odaklandığı disiplinlerarası bir çalışma olan 3 boyutlu (3B) biyobasım tekniği en yenilikçi teknolojilerden biridir. 3 boyutlu biyobasım, yaralı veya hastalıklı doku ve organları biyolojik olarak taklit edebilecek (biomimetik) doku ve organların yapımında çeşitli uygulamalara sahip gelişmekte olan bir teknolojidir. Bu yöntemde hücreler, büyüme faktörleri ve biyomalzemeler birleştirilir ve hibrit bir biyomalzeme elde edilir. Biyomalzemeler vasıtasıyla canlı hücreler ile katman katman, istenilen şekil, miktar ve fonksiyonda hücre iskeletleri (scaffold) üretilebilir. Özellikle karaciğer gibi karmaşık dokuları oluşturmak için biyobasım tekniği ile doku iskeleleri oluşturmak oldukça önemli bir yaklaşımdır. Hem doğal hem de sentetik kökenli polimerlerden yapılan biyo bağlantılar, karaciğer gibi yumuşak dokulara baskı uygulanması noktasında avantaja sahiptir. Bu derlemede özellikle hepatositler üzerine yapılan çalışmalar incelenmiş ve derlenmiştir.Yayın MECHANICAL STIFFNESS OF PEGDA BASED HYDROGELS AFFECTS FORMATION OF HEPG2 SPHEROIDS IN 3D SCAFFOLDS(Wiley, 2021) Ulugöl, R. K.; Demirel, Gamze; Akbulut, Zeynep; Yener, Nese; Tok, Olgu Enis; Decker, Heather; Mellot, A. J.[Abstract Not Available]
