PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Editorial Editorial: Advancing Biotechnology in Turkiye: a Dedication To All Women(Springer, 2025) Cadirci, Bilge Hilal; Buyukkileci, Ali Oguz; Binay, BarisArticle Influence of Soil Characteristics on the Phytochemistry of Evergreen Ivy (Hedera Helix L.) Leaves in Deciduous Forests(Wiley-v C H verlag Gmbh, 2025) Yildirim, Elif Begum; Ozer, Gulcin; Sen, Nisa Beril; Ozdemir, Emrah; Makineci, Ender; Ozdemir, Durmus; Guzelmeric, EtilThe evergreen ivy (Hedera helix L.), traditionally used to treat respiratory conditions, contains triterpene saponins, primarily hederacoside C, and various phenolic compounds. This study investigated the relationships between the chemical composition of ivy leaves and their natural growing conditions (moisture, temperature, pH, and electrical conductivity of soil). Ivy leaves were collected monthly over 1 year from oak and beech forests. Hederacoside C, rutin, chlorogenic acid (ChA), neoChA, 4,5-dicaffeoylquinic acid (DCQA), and 3,5-DCQA were analyzed by high-performance thin-layer chromatography (HPTLC) and high-performance liquid chromatography (HPLC). Soil parameter data, along with the quantitative HPLC results of ivy leaves, were first subjected to bivariate analysis, which revealed significant correlations, particularly between soil moisture, soil temperature, and the chemical composition of ivy leaves. In addition, ivy samples were classified and clustered based on seasons by principal component analysis (PCA) and hierarchical cluster analysis (HCA), regardless of their collection sites. Digitized HPTLC chromatograms were evaluated by PCA and partial least squares discriminant analysis (PLS-DA) analyses; PCA enabled the grouping of ivy leaves based on their collection sites, and PLS-DA categorized the samples by seasons. The evaluation of the relationships between the phytochemistry of ivy leaves and their natural growing conditions has been reported for the first time.Article Citation - WoS: 5Citation - Scopus: 7Targeting the Panoptosome Using Necrostatin-1 Reduces Panoptosis and Protects the Kidney Against Ischemia-Reperfusion Injury in a Rat Model of Controlled Experimental Nonheart-Beating Donor(Elsevier Science inc, 2024) Dokur, Mehmet; Uysal, Erdal; Kucukdurmaz, Faruk; Altinay, Serdar; Polat, Sait; Batcioglu, Kadir; Yeni, Sema Nur DokurPurpose. Reducing renal ischemia is crucial for the function and survival of grafts from non- heartbeat donors, as it leads to inflammatory responses and tubulointerstitial damage. The primary concern with organs from nonheartbeat donors is the long warm ischemia period and reperfusion injury following renal transplantation. This study had two main goals; one goal is to determine how Necrostatin-1 targeting the PANoptosome affects PANoptosis in the nonheartbeating donor rat model. The other goal is to fi nd out if Necrostatin-1 can protect the kidney from ischemic injury for renal transplantation surgery. Methods. Twenty-four rats were grouped randomly as control and Necrostatin-1 in this experimental animal study, and we administered 1.65 mg/kg of Necrostatin-1 intraperitoneally to the experimental group for 30 minutes before cardiac arrest. We removed the rats' left kidneys and measured various oxidative stress marker measures such as malondialdehyde, superoxide dismutase, catalase, GPx, and 8-hydroxy-2-deoxyguanosine levels. We then subjected the tissues to immunohistochemical analysis, electron microscopy, and histopathological analysis. Findings. The Necrostatin-1 group had a lower total tubular injury score (P < .001) and less Caspase-3, gasdermin D, and mixed lineage kinase domain-like protein expression. Additionally, the apoptotic index of the study group was lower (P < .001). Furthermore, the study group had higher levels of superoxide dismutase and GPx (P < .05), whereas malondialdehyde levels were reduced (P = .009). Electron microscopy also revealed a significant improvement in tissue structure in the Necrostatin-1 group. Conclusion. Necrostatin-1 protects against ischemic acute kidney injury in nonheart-beating donor rats by inhibiting PANoptosis via the blockade of RIPK1. As a result of this, Necrostatin1 may offer novel opportunities for protecting donor kidneys from renal ischemia-reperfusion injury during transplantation in patients with end-stage kidney disease requiring a renal transplantation.Article Comprehensive Analysis Of<i> Gjb1</I> in Breast Cancer: Its Implications in Survival and Molecular Mechanisms(int inst Anticancer Research, 2024) Ozcivici, Engin; Mese, GulistanBackground/Aim: Breast cancer is the leading cause of cancer-related mortality among women worldwide. The connexin (Cx) family, including GJB1 (Cx32), plays complex roles in tumor progression depending on cellular context and cancer subtype. While Cx32 overexpression has been linked to lymph node metastasis, its effects on survival and molecular processes remain unclear. Herein, we aimed to investigate the role of GJB1 in breast cancer by examining its impact on survival and cellular processes in addition to its expression pattern in tumor subtypes, using public datasets. Materials and Methods: We conducted a comprehensive analysis of GJB1 in breast cancer using METABRIC patient dataset, Cancer Cell Line Encylopedia, and other publicly available databases. We examined the association between GJB1 expression and patient survival, performed differential gene expression analysis, and explored gene set enrichment to identify biological processes associated with high GJB1 expression. Results: GJB1 was significantly down-regulated in breast cancer tissues compared to normal tissues. However, patients with high GJB1 expression had significantly poorer survival compared to those with low expression, with the median survival reduced by over 25 months. Gene ontology (GO) analysis revealed that down- regulated genes in the GJB1-high group were enriched in extracellular matrix components and membrane junctions, while up-regulated genes were associated with mitochondrial function and cellular respiration. Conclusion: Our findings suggest a dual role for GJB1 in breast cancer. Although it is generally down-regulated, high GJB1 expression is associated with poorer survival, implying a potential oncogenic role. Further studies are needed to clarify the role of GJB1 in breast cancer and explore its therapeutic implications.Article Citation - WoS: 2Citation - Scopus: 2Exploring the Use of Water-Extracted Flaxseed Hydrocolloids in Three-Dimensional Cell Culture(Mary Ann Liebert, inc, 2024) Yildirim-Semerci, Ozum; Bilginer-Kartal, Rumeysa; Arslan-Yildiz, AhuPlant-derived hydrocolloids offer promising prospects in biomedical applications. Among these, Flaxseed hydrocolloid (FSH) can form a soft, elastic, and biocompatible hydrocolloid with tunable viscosity and superior swelling capacity, making it an attractive scaffold. This study introduces a green extraction method for FSH, employing a single-step aqueous extraction process and fabrication of FSH scaffold. Despite growing interest, the pristine form of FSH has not been investigated for sustainable long-term three-dimensional (3D) cell culture. Here, FSH scaffolds were thoroughly characterized for their morphological, chemical, mechanical, and biological properties. 3D cell culture experiments were conducted using NIH-3T3 mouse fibroblast cells, and cell viability was assessed using live/dead and Alamar Blue assays. High cell viability was sustained for long term compared with 2D cell culture. Cell adhesion and 3D cellular morphology on FSH scaffold for 30 days were monitored by scanning electron microscopy analysis. Also, collagen type-I and F-actin expressions were analyzed by immunostaining after 30 days of culture, resulting in 5- and 4-fold increments of fluorescence intensity, respectively. Results indicate sustained cell viability in the long term and favorable cell-material interaction, demonstrating the potential of FSH as a scaffold. This study emphasizes the importance of the green extraction approach, improving the biocompatibility and functionality of FSH tissue engineering applications. Impact Statement Flaxseed hydrocolloid (FSH) is a promising scaffold for biomedical applications due to its biocompatibility and tunable properties. This study introduces a green extraction method for FSH and evaluates its use in 3D cell culture with NIH-3T3 mouse fibroblast cells. The findings indicate high cell viability and enhanced cell-material interactions over 30 days, highlighting the potential of FSH for tissue engineering.Article Citation - WoS: 2Citation - Scopus: 2Mapk Pathway and Nis in B-Cpap Human Papillary Thyroid Carcinoma Cells Treated With Resveratrol(Elsevier Gmbh, 2024) Kocabas, Gokcen Unal; Blatti, Asli Kisim; Berdeli, Afig; Ozgen, Ahmet Gokhan; Yurekli, Banu SarerBackground: Resveratrol, a herbal phytoalexin, is known to have anti-tumor effects in several tumors including thyroid cancer cells. Aim: The aim of this study was to determine the effects of resveratrol on the expression of BRAF, ERK and NIS mRNA levels and protein expression in B-CPAP human thyroid papillary cancer cell line. Methods: B-CPAP cells were treated with resveratrol at concentrations of 10-100 mu M for 24-48-72 h. Cell viability was assessed by XTT Cell Proliferation Assay. BRAF, ERK and NIS mRNA levels were evaluated by rtPCR method. Protein expressions were evaluated by Western Blot method. Results: Resveratrol was found to inhibit cell proliferation in a time and dose dependent manner. The IC50 values of resveratrol were 18.7 mu M and 56.8 mu M after 48 h and 72 h respectively. Resveratrol treatment of B-CPAP cells resulted in up to 1.5-fold reduction in BRAF mRNA and up to 5.5 fold reduction in ERK mRNA levels. NIS mRNA levels showed up to 3-fold increase. Western Blot studies confirmed the rt- PCR results with a decrease in BRAF and ERK, and increase in NIS protein expressions. Conclusion: This study demonstrated that resveratrol inhibits thyroid papillary carcinoma cell proliferation and reduces poor prognostic BRAF and ERK mRNA and protein expressions, while increasing NIS mRNA and protein expression suggesting a redifferentiating effect. More studies are needed to evaluate resveratrol as a novel therapeutic agent in the treatment of papillary thyroid cancer.Article Citation - Scopus: 27Apoptotic Effects of Resveratrol, a Grape Polyphenol, Onimatinib-Sensitive and Resistant K562 Chronic Myeloid Leukemia Cells(2012) Can,G.; Cakir,Z.; Kartal,M.; Gunduz,U.; Baran,Y.Aim: To examine the antiproliferative and apoptotic effects of resveratrol on imatinib-sensitive and imatinib-resistant K562 chronic myeloid leukemia cells. Materials and Methods: 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). Results: The concentrations of resveratrol that inhibited cell growth by 50% ( IC50) 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. Conclusion: 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: 1Citation - Scopus: 1Canine Oocyte Nuclear Maturation With Nano-Ozone (nzs) Supplementation: the Alterations of Antioxidant, and Oxidant Status and Cdk1, Cyclin B1 Expressions(Elsevier, 2024) Bari, O.; Sabanci, A. U.; Avci, G.; Bozkurt, B.; Ustuner, B.; Denk, B.; Ozalp, G. R.This study aims to evaluate the effects of nano-ozone solution (NZS) on canine oocyte nuclear maturation, associated with the alterations of antioxidant and oxidant status and cyclin-dependent kinase 1 (CDK1), cyclin B1 gene expressions. Oocytes were cultured in four distinct concentrations of NZS (0.5, 1, 2, and 5 mu g/mL) and parthenogenetically activated. The rates of oocytes arrested at the Germinal Vesicle (GV), Germinal Vesicle Breakdown (GVBD), Metaphase I (MI), and Metaphase II (MII) stages were statistically different among groups (P < 0.05). The oocytes cultured in 1 <mu>g/mL NZS yielded the best oocyte maturation rate at the MI and MII stages; however, the lowest maturation and high degeneration rates were observed in Group E. The measurements of Malondialdehyde (MDA), reduced Glutathione (GSH), Superoxide Dismutase (SOD), and Ferric Reducing/Antioxidant Power assay (FRAP) were performed from IVM culture media. No statistical difference was observed in SOD and MDA results (P > 0.05). GSH levels were statistically significant between Group AGroup E (p = 0.003), Group B-Group E (p = 0.045), and Group E-Group D (p = 0.021). The culture media in Group D and Group E had high FRAP concentrations and significantly differed between groups (P < 0.05). CDK1, and cyclin B1 genes, which are subunits of maturation-promoting factor (MPF), are upregulated in Group B and Group C, while are downregulated in oocytes of Group E. This study showed that low, controlled doses of NZS (1 <mu>g/mL) supplementation could improve the meiotic competence of canine oocytes and lead to positive response in expressions of CDK1 and cyclin B1 on the gene level.Article Genetic Factors Associated With Age-Related Macular Degeneration Modulating Plasma Inflammatory Biomarker Levels in Patients With Aids(Taylor & Francis inc, 2024) Sezgin, Efe; Schneider, Michael F.; Hunt, Peter W.; Beck-Engeser, Gabriele; Ambayac, Gabriele C.; Jabs, Douglas A.IntroductionPatients with the acquired immunodeficiency syndrome (AIDS) have an increased prevalence and incidence of intermediate-stage age-related macular degeneration (AMD). Several elevated plasma inflammatory biomarkers are associated with increased incidence of intermediate-stage AMD in this population. We evaluated the association between AMD risk alleles and plasma inflammatory biomarker levels in persons with AIDS.Materials and MethodsCryopreserved plasma specimens of 229 non-Hispanic White and 252 non-Hispanic blacks from the Longitudinal Study of the Ocular Complications of AIDS cohort were assayed for plasma levels of soluble tumor necrosis factor receptor (sTNFR) 2, interleukin (IL)-18, C x 3motif chemokine ligand 1 (CX3CL1), C-reactive protein (CRP), and soluble CD14 (sCD14). Genotyping included AMD-associated variants rs10801553 and rs800292 for complement factor H (CFH) rs9332739 and rs547154 for complement factor 2 (C2), rs2230199 for C3, rs2285714 for CFI, and rs3732379 and rs3732378 for C x 3motif chemokine receptor 1 (CX3CR1).ResultsIn Whites, AMD low-risk CX3CR1 variants (V249I and T280M) were associated with reduced plasma levels of IL-18. In Blacks, AMD low-risk C3 R102G and low-risk CX3CR1 T280M variants were associated with reduced CRP levels.ConclusionsGenetic variants in AMD-associated immune genes may influence AMD-associated systemic plasma inflammatory biomarker levels in patients with AIDS.Article Citation - WoS: 7Citation - Scopus: 8Investigation of Stair Ascending and Descending Activities on the Lifespan of Hip Implants(Elsevier Sci Ltd, 2024) Alpkaya, Alican Tuncay; Yilmaz, Mehmet; Sahin, Ahmet Mert; Mihcin, SenayTotal hip arthroplasty (THA) surgeries among young patients are on the increase, so it is crucial to predict the lifespan of hip implants correctly and produce solutions to improve longevity. Current implants are designed and tested against walking conditions to predict the wear rates. However, it would be reasonable to include the additional effects of other daily life activities on wear rates to predict convergent results to clinical outputs. In this study, 14 participants are recruited to perform stair ascending (AS), descending (DS), and walking activities to obtain kinematic and kinetic data for each cycle using marker based Qualisys motion capture (MOCAP) system. AnyBody Modeling System using the Calibrated Anatomical System Technique (CAST) full body marker set are performed Multibody simulations. The 3D generic musculoskeletal model used in this study is a markerbased full-body motion capture model (AMMR,2.3.1 MoCapModel) consisting of the upper extremity and the Twente Lower Extremity Model (TLEM2). The dynamic wear prediction model detailing the intermittent and overall wear rates for CoCr-on-XLPE bearing couple is developed to investigate the wear mechanism under 3D loading for AS, DS, and walking activities over 5 million cycles (Mc) by using finite element modelling technique. The volumetric wear rates of XLPE liner under AS, DS, and walking activities over 5-Mc are predicted as 27.43, 23.22, and 18.84 mm3/Mc respectively. Additionally, the wear rate was predicted by combining stair activities and gait cycles based on the walk-to-stair ratio. By adding the effect of stair activities, the volumetric wear rate of XLPE is predicted as 22.02 mm3/Mc which is equivalent to 19.41% of walking. In conclusion, in this study, the effect of including other daily life activities is demonstrated and evidence is provided by matching them to the clinical data as opposed to simulator test results of implants under ISO 14242 boundary conditions.
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