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Öğe Advancing glioblastoma research: A comparative study of drug response in novel 3D pHEMA-gelatin cryogel and traditional 2D models(Springer Heidelberg, 2025) Alkis, Meryem Damla Ozdemir; Pesint, Gozde Baydemir; Gokturk, DilekGlioblastoma (GBM) is the most abundant and malignant type of brain tumors. Investigating and understanding GBM biology is crucial for developing new treatments. This study aims to establish a novel 3D GBM cell culture model to investigate the drug response and comprehend GBM tumor biology. pHEMA-gelatin based cryogels are synthesized by varying cryogelation temperatures and gelatin concentrations to design a suitable scaffold. Characterization studies and in vitro cell studies show that all synthesized cryogels can be used as scaffolds for GBM, however pHEMA-gelatin-based cryogel synthesized at - 16 degrees C with 2% (w/w) gelatin concentration gave the highest cell viability test result with 221% in 3-day culture. The drug response assay is also performed by applying etoposide and temozolomide separately on GBM scaffolds by comparing 2D cultured cells. It is observed that GBM cells cultured on this cryogel exhibit greater resistance to drugs than 2D cultured cells.Öğe An alternative approach to tracing the volumic proliferation development of an entire tumor spheroid in 3D through a mini-Opto tomography platform(Pergamon-Elsevier Science Ltd, 2022) Polat, Adem; Gokturk, DilekMicroscopy, which is listed among the major in-situ imaging applications, allows to derive information from a biological sample on the existing architectural structures of cells and tissues and their changes over time. Large biological samples such as tumor spheroids cannot be imaged within one field of view, regional imaging in different areas and subsequent stitching are required to attain the full picture. Microscopy is not typically used to produce full-size visualization of tumor spheroids measuring a few millimeters in size. In this study, we propose a 3D volume imaging technique for tracing the growth of an entire tumor spheroid measuring up to 10 mm using a miniaturized optical (mini-Opto) tomography platform. We performed a primary analysis of the 3D imaging for the MIA PaCa-2 pancreatic tumoroid employing its 2D images produced with the mini-Opto tomography from different angles ranging from -25 degrees to +25 degrees at six different three-day-apart time points of consecutive image acquisition. These 2D images were reconstructed by using a 3D image reconstruction algorithm that we developed based on the algebraic reconstruction technique (ART). We were able to reconstruct the 3D images of the tumomid to achieve 800 x 800-pixel 50-layer images at resolutions of 5-25 mu m. We also created its 3D visuals to understand more clearly how its volume changed and how it looked over weeks. The volume of the tumor was calculated to be 6.761 mm(3) at the first imaging time point and 46.899 mm(3) 15 days after the first (at the sixth time point), which is 6.94 times larger in volume. The mini-Opto tomography can be considered more advantageous than commercial microscopy because it is portable, more cost-effective, and easier to use, and enables full-size visualization of biological samples measuring a few millimeters in size.Öğe Assessment of L-methioninase in volatile sulfur compound-rich Cheddar cheese slurries: bacterial community profiling via next-generation sequencing(Taylor & Francis Ltd, 2025) Ipek, Semih Latif; Gokturk, DilekIn this study, sulfur-containing aroma compounds and the associated shifts in bacterial community composition following the addition of L-methioninase to cheddar cheese slurries were examined. Four distinct slurry formulations were prepared: a control, a methionine-supplemented control, and two experimental groups supplemented with either L-methioninase or Brevibacterium linens. On day 1, Lactococcus and Streptococcus species were dominant across all samples. By day 9, bacterial diversity increased markedly in all formulations. On the first day of fermentation, L-methioninase activity led to the production of 1731.0 +/- 1.09 mu g kg-1 dry matter of methanethiol and 1490.2 +/- 1.31 mu g kg-1 dry matter of dimethyl trisulfide (DMTS). The concentrations of both methanethiol and DMTS increased further on days 4 and 9 of fermentation. These findings suggest that the use of L-methioninase in cheese slurries may represent a promising alternative strategy for the production of enzyme-modified cheese with enhanced sulfur aroma profiles.Öğe Comparison of additive effects on the PVA/starch cryogels: Synthesis, characterization, cytotoxicity, and genotoxicity studies(Taylor & Francis As, 2018) Ceylan, Seda; Gokturk, Dilek; Demir, Didem; Ozdemir, M. Damla; Bolgen, NimetThe research goal of this study is to produce suitable scaffolds for tissue engineering applications. Different ratios of polyvinyl alcohol (PVA)/starch (90:10, 70:30, 50:50) and crosslinking methods have been used to prepare cryogels. Chemically crosslinked cryogels were synthesized using glutaraldehyde as the crosslinking agent. For the physically crosslinked cryogels, sodium dodecyl sulfate was used during cryogelation as the foaming agent. Chemical structure and pore morphology were demonstrated by Fourier transform infrared spectroscopy and scanning electron microscopy (SEM). Swelling ratio and degradation profile of the scaffolds were also determined. 3-(4,5-dimethylthiazoyl-2-yl)-2,5-diphenyltetrazolium bromide assay and SEM were used to investigate the biocompatibility of the scaffolds and cell morphology. Genotoxicity test was performed to show DNA fragmentation. The overall results demonstrated that PVA/starch cryogels could have potentially appealing application as scaffolds for tissue engineering applications and additives affect the architecture and characteristic properties of the cryogels. [GRAPHICS] .Öğe Cytotoxic Effect of L-Methioninase from Brevibacterium linens BL2 in Combination with Etoposide against Glioblastoma Cells(Mdpi, 2023) Ipek, Semih Latif; Ozdemir, Meryem Damla; Gokturk, DilekL-methioninase degrades methionine, which is essential in methionine-dependent cancer cells, resulting in specific cell death. Normal cells can synthesize their own methionine amino acids even in the absence of exogenous methionine. This selective targeting of cancer cells makes L-methioninase a promising therapeutic candidate for cancer. In this study, L-methioninase was partially purified from Brevibacterium linens BL2. The specific activity of the enzyme was found as 3.055 units/mg. IC50 values (24 h) of the enzyme were 5.792 units/mL for U87MG cell line and 5.215 units/mL for T98G cell line. When L-methioninase and etoposide were used in combination, synergistic cytotoxic and cell migration inhibition effects on U87MG and T98G cells alongside decreased cytotoxic activity on the Mouse Embryonic Fibroblast and HaCaT cells compared to etoposide alone were observed. Additionally, colony numbers of U87MG cells were significantly reduced by L-methioninase and etoposide administration after 21 days of incubation. Furthermore, L-methioninase suppressed the expression levels of survivin and c-Myc while increasing the expression level of Caspase-3 in both glioblastoma cell lines. These effects were enhanced when etoposide was used in combination with etoposide. This investigation reveals that the L-methioninase enzyme not only exhibited cytotoxic effects on U87MG and T98G cells but also enhanced the anti-proliferative effects of etoposide when used in combination while also demonstrating fewer adverse effects on normal cells.Öğe Effect of crosslinking methods on the structure and biocompatibility of polyvinyl alcohol/gelatin cryogels(Ios Press, 2016) Ceylan, Seda; Gokturk, Dilek; Bolgen, NimetIn this study, polyvinyl alcohol (PVA) and gelatin based cryogels were prepared by crosslinking chemically or physically for tissue engineering applications. Different PVA/Gelatin ratios (100: 0, 90: 10, 70: 30, 50: 50) and crosslinking methods have been used to prepare cryogels; chemical and physical structure of the prepared matrices were analysed by FTIR and SEM; swelling and degradation profiles were followed. Chemical and physical crosslinking was obtained by using glutaraldehyde as crosslinker and by applying freeze thawing cycle, respectively. Gelatin concentration and crosslinking method had significant effect on the pore size, swelling ratio and degradation profiles of the cryogels. Biocompatibility of the cryogels were also investigated by MTT assay. SEM was used to investigate the cell morphology on the scaffolds. The MTT assay findings prove that physically crosslinked PVA/Gelatin scaffolds are more biocompatible and enhance more the adhesion and proliferation of mouse embryonic fibroblast cells (MEF) than chemically crosslinked PVA/Gelatin scaffolds. The overall results demonstrated that, the PVA/Gelatin cyrogels as a suitable biomaterial for tissue engineering applications and crosslinking methods affect the architecture and characteristic properties of the cryogels.Öğe Effects of Juniperus drupacea concurrent with etoposide on glioblastoma cell culture(Elsevier, 2023) Gokturk, Dilek; Alkis, Meryem Damla OzdemirGlioblastoma (GBM) is a prevalent and most malignant kind of glioma, reported as grade IV glioma by the World Health Organization. In a year 3-10 per 100.000 people are diagnosed with GBM and their mean life expectancy could only be 12-16 months after diagnosis.Juniperus drupacea, a member of the Cupressaceae family is a medicinal herb. In this study, the free radical scavenging activity and volatile components of Juniperus drupacea were analyzed and the cytotoxic effects of Juniperus drupacea molasses and cone seed extract in combination with etoposide on GBM cell line (U-87 MG (ATCC (R) HTB-14TM)) were evaluated. Furthermore, the impact of Juniperus drupacea extract on the migration capacity of GBM cells was examined. Based on the DPPH radical scavenging activity assay, the amount of free radical-binding antioxidants in the Juniperus drupacea extract was found to be 0.575 mg/mL Trolox equivalent. The results of the cytotoxicity and migration assays revealed that Juniperus drupacea reduced the viability and migration capacity of GBM cells and increase the cytotoxic effect of etoposide. Considering these findings, it was hypothesized that some of the components of Juniperus drupacea might have possible therapeutic effects for the treatment of glioblastoma.(c) 2023 SAAB. Published by Elsevier B.V. All rights reserved.Öğe Extraction of pectin from albedo of lemon peels for preparation of tissue engineering scaffolds(Springer, 2021) Demir, Didem; Ceylan, Seda; Gokturk, Dilek; Bolgen, NimetPectin is a type of anionic polysaccharide naturally found in a number of fruits and vegetables. Although pectin is widely used for food industry, its biomedical applications such as wound dressing, drug delivery and cancer targeting have also been investigated. In our study, we combined extracted pectin (from albedo of lemon peels) with chitosan (as a natural polymer) to synthesize chitosan/pectin cryogels. The extracted pectin was subjected to qualitative and quantitative analyses. Chitosan/pectin spongy supermacroporous cryogels were produced by cryogelation method at different combinations (100:0, 80:20, 60:40 and 40:60, w/w). Polyelectrolyte interactions between pectin and chitosan and crosslinking of chitosan with glutaraldehyde were verified by using FTIR. The porosity, swelling ratio, degradation behaviors and mechanical properties of cryogels were determined. SEM analysis demonstrated the pore morphology and average pore diameters of cryogels. After all analysis, 40:60 chitosan/pectin cryogel was selected for cytotoxicity studies. Glioblastoma (U-87 MG) cell line was used to evaluate the in vitro cytotoxicity of scaffolds. MTT assay and SEM analyses demonstrated the scaffolds were nontoxic, and supported cell attachment and viability.Öğe Non-Detection of HCMV Total Genomic DNA in Human Glioma Cells Genome(Turkish Neurosurgical Soc, 2024) Gokturk, Dilek; Alkis, M. Damla Ozdemir; Yilmaz, Dervis MansuriAIM: To demonstrate if the human cytomegalovirus (HCMV) genome, that is involved in the pathogenesis of gliomas, is part of the genomic DNA of glioma cells or not. MATERIAL and METHODS: The study included U87MG glioblastoma cell culture and tumor samples from glioma patients. The genomic DNA of tumor samples and U87MG cells were extracted and real-time quantitative PCR was used to assess the presence of the human cytomegalovirus genomic DNA. RESULTS: Consequently, HCMV positivity was not detected in the tumor and cell line genomic DNA under the aforementioned experimental conditions. CONCLUSION: We found that the genomic DNA of all the samples was negative for HCMV genomic DNA. Thus, HCMV could not be detected in human glioma tumors and we put forward that HCMV genomic DNA was not incorporated into the genomic DNA of glioma cells. Thus, total viral DNA is not involved in the pathogenesis of glioma; however, small viral particles or specific genes might be incorporated into the genomic DNA of glioma cells, leading to cancer development. This prompts further studies for verification.Öğe Production of L-asparaginase from Candida utilis by solid-state fermentation: a comprehensive assessment of its antiproliferative potential on glioblastoma cells(Springer, 2025) Alkis, Meryem Damla Ozdemir; Ipek, Semih Latif; Tulek, Ahmet; Gunduz, Cennet Pelin Boyaci; Gokturk, DilekL-asparaginase (L-ASNase) is an enzyme that depletes asparagine, a key amino acid for cancer cell survival, producing aspartic acid and ammonia. Beyond its food industry applications, L-ASNase is a clinically important agent against acute lymphoblastic leukemia (ALL). In this study, L-ASNase was produced and purified from Candida utilis via solid-state fermentation. Optimization on wheat bran identified 2 mL inoculation volume, 60% moisture, and a 4-day fermentation period as the optimal conditions, yielding 172.5 U/mL activity. The purified enzyme was tested against glioblastoma (GBM) cell lines, showing IC50 values of 0.4 U/mL for U87MG and 1.8 U/mL for T98G, with minimal toxicity toward normal HaCaT cells. Apoptotic effects were confirmed by DAPI/F-actin and Giemsa staining, while wound healing and clonogenic assays revealed inhibition of cell migration and colony formation. RT-qPCR analysis demonstrated downregulation of the Survivin gene, a key survival regulator. These findings highlight L-ASNase's potent antiproliferative, anti-migratory, and pro-apoptotic effects, underscoring its potential as an adjuvant therapy for GBM.Öğe Recombinant Expression of L-methioninase from Brevibacterium linens and Evaluation of its Anticarcinogenic Properties against MiaPaCa-2 Cells(Bentham Science Publ Ltd, 2025) Ipek, Semih Latif; Alkis, Meryem Damla Ozdemir; Tulek, Ahmet; Gokturk, DilekIntroduction This study aimed to investigate the anti-carcinogenic effects of recombinant L-methioninase (rBlmet) on the pancreatic cancer cell line MiaPaCa-2.Methods In this study, rBlmet was initially cloned, expressed, and purified. To increase enzyme activity, the His-tags on the enzyme were removed using thrombin. rBlmet was then applied to MiaPaCa-2 cells, and the cell viability of MiaPaCa-2 cells was evaluated by neutral red assay after rBlmet treatment. The combined effect of etoposide with rBlmet against MiaPaCa-2 cells was also evaluated for 12 and 24 hours using a neutral red assay. Furthermore, cell morphology was evaluated by Giemsa and DAPI/F-actin staining methods. Survivin and caspase-3 gene expression levels were measured by RT-qPCR.Results and Discussion The specific activity of the enzyme increased after His-tag elimination to 5.62 mu mol/mg per minute. rBlmet showed a significant cytotoxic effect on the MiaPaCa-2 cell line. The IC50 value (24 h) of rBlmet for MiaPaCa-2 cells was 3.02 U/mL. In addition, rBlmet increased the cytotoxic effect of etoposide on the MiaPaCa-2 cell line, while it showed less effect on HaCat, which is a normal human cell line. Furthermore, rBlmet increased caspase-3 expression and downregulated survivin gene expression in MiaPaCa-2 cell lines.It successfully inhibited the growth of Mia-PaCa-2 cells by exploiting exogenous methionine amino acid in the growth medium. This study revealed promising results. However, further studies are needed on additional pancreatic cancer cell lines and in vivo models.Conclusion Based on these findings, it can be concluded that rBlmet not only has great potential to treat pancreatic cancer in the future but can also be used as an adjuvant to enhance the effectiveness ofchemotherapeutic agents like etoposide.Öğe Tailoring the spatial filament organization within nanofibrous tissue engineering scaffolds(Taylor & Francis As, 2022) Shah Hosseini, Neda; Bolgen, Nimet; Khenoussi, Nabyl; Ceylan, Seda; Gokturk, Dilek; Schacher, Laurence; Adolphe, DominiqueFabricating scaffolds with biomimetic architectures is an important step toward engineering functional tissues. Electrospinning is a popular approach for creating nanofibrous substrates in which the filaments resembling the natural extracellular matrix (ECM) can provide topographical cues to cells directing their growth. One of the major challenges in electrospinning is tailoring the spatial organization of the filaments. To overcome this challenge, a hybrid static collector was utilized to form distinct filament organizations. The filament organization was characterized using image processing based on the Fourier Transforms Method. The effect of different filament orientation ratios on cellular growth is discussed.Öğe The concurrent effect of acyclovir and rosemary on glioblastoma cell culture(C M B Assoc, 2019) Ozdemir, Meryem Damla; Gokturk, DilekHuman cytomegalovirus (HCMV) is a beta herpesvirus which large amount of people in world has interacted with. Recent studies indicated that CMV DNA is associated with several cancer types including Glioblastoma (GBM) which is the most common and aggressive type of primary brain cancer. In clinical studies it was shown that several antiviral medicines prolonged life span of glioblastoma patients. One of them is Acyclovir (ACV) which is a type of nucleoside analog, used to cure viral infections and might be a potential treatment supplement for Glioblastoma. In this study we aimed to investigate if ACV had cytotoxic effect on glioblastoma cell line U87 MG and also the effect of ACV on healthy cells. Furthermore it was aimed to search the effect of Rosmarinus Officinalis also known as rosemary which is an aromatic, perennial plant concurrent with ACV on glioblastoma and healthy cells.Öğe The Effect of Ascorbic Acid over the Etoposide- and Temozolomide-Mediated Cytotoxicity in Glioblastoma Cell Culture: A Molecular Study(Turkish Neurosurgical Soc, 2018) Gokturk, Dilek; Kelebek, Haşim; Ceylan, Seda; Yilmaz, Dervis MansuriAIM: Glioblastoma (GBM) is one of the lethal central nervous system tumors. One of the widely used chemical agents for the treatment of glioblastoma is temozolomide. It is an orally administered, deoxyribonucleic acid (DNA) alkylating agent. DNA alkylation triggers the death of tumor cells. However, some tumor cells are able to repair this type of DNA damage and thus lower the therapeutic effect of temozolomide. Laboratory and clinical studies indicate that temozolomide's anticancer effects might be strengthened when combined with other chemotherapeutic agents like etoposide or antioxidant agents like ascorbic acid. In this study, we aimed to evaluate the cytotoxic and oxidative stress effects of ascorbic acid (1000 mu M), temozolomide (100 mu M) and etoposide (25 mu M) agents alone and in dual and triple combinations in a glioblastoma U87 MG cell culture. MATERIAL and METHODS: The cytotoxic and oxidative stress effects were investigated by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis methods. RESULTS: Cytotoxicity tests showed that etoposide, temozolomide, etoposide+ascorbic acid, temozolomide+ascorbic acid, temozolomide+etoposide and temozolomide+etoposide+ascorbic acid combinations have anti-proliferative effects. The maximum anti-proliferation response was observed in the temozolomide+etoposide+ascorbic acid-added group. Similarly LCMS/MS analyses showed that minimum oxidative DNA damage occurred in the temozolomide+etoposide+ascorbic acid-added group. CONCLUSION: Ascorbic acid decreases the cytotoxic and genotoxic effect of etoposide and etoposide-temozolomide combination but it has no meaningful effect on temozolomide's toxicity.Öğe The Effect of Rosmarinus Officinalis and Chemotherapeutic Etoposide on Glioblastoma (U87 MG) Cell Culture(Turkish Neurosurgical Soc, 2018) Ozdemir, Meryem Damla; Gokturk, DilekAIM: To investigate whether high dose toxicities of etoposide can be overcome when used in combination with a natural compound named Rosmarinus Officinalis for glioblastoma (GBM). MATERIAL and METHODS: The impact of Rosmarinus Officinalis in combination with etoposide on GBM U87 MG cells and Mouse Embryonic Fibroblast (MEF) cells was investigated. Both neutral red and 3-(4, 5-Dimethylthiazol-2-Yl)-2, 5-Diphenyltetrazolium Bromide (MTT) assays were employed to gauge cell viability. RESULTS: We observed that increased quantities of Rosmarinus Officinalis induced MEF cell proliferation while it inhibited the survival of GBM cells. Our results indicate that Rosmarinus Officinalis did not affect the cytotoxicity of etoposide on GBM cell cultures. In contrast, in the MEF cell cultures, Rosmarinus Officinalis induced proliferation and diminished the impact of etoposide. CONCLUSION: Rosmarinus Officinalis offers hope for developing new cancer treatment strategies. However, further studies are needed to verify these results.Öğe Tracing 2D Growth of Pancreatic Tumoroids Using the Combination of Image Processing Techniques and Mini-Opto Tomography Imaging System(Sage Publications Inc, 2023) Akbaba, Cihat Ediz; Polat, Adem; Gokturk, DilekObjectives: In this study, we aimed to trace the 2D growth development of tumoroids produced with MIA PaCa-2 pancreatic cancer cells at different time points. Methods We cultured 3 different tumoroids with 0.5%, 0.8%, and 1.5% agarose concentrations and calculated the growth rate of the tumoroids with their images acquired at 9 imaging time points by mini-Opto tomography imaging system applying image processing techniques. We used the metrics contrast-to-noise ratio (CNR), peak signal-to-noise ratio (PSNR), and mean squared error (MSE) to analyze the distinguishability of the tumoroid structure from its surroundings, quantitatively. Additionally, we calculated the increase of the radius, the perimeter, and the area of 3 tumoroids over a time period. Results In the quantitative assessment, the bilateral and Gaussian filters gave the highest CNR values (ie, Gaussian filter: at each of 9 imaging time points in range of 1.715 to 15.142 for image set-1). The median filter gave the highest values in PSNR in the range of 43.108 to 47.904 for image set-2 and gave the lowest values in MSE in the range of 0.604 to 2.599 for image set-3. The areas of tumoroids with 0.5%, 0.8%, and 1.5% agarose concentrations were 1.014 mm(2), 1.047 mm(2), and 0.530 mm(2) in the imaging time point-1 and 33.535 mm(2), 4.538 mm(2), and 2.017 mm(2) in the imaging time point-9. The tumoroids with 0.5%, 0.8%, and 1.5% agarose concentrations grew up to times of 33.07, 4.33, and 3.80 in area size over this period, respectively. Conclusions The growth rate and the widest borders of the different tumoroids in a time interval could be detected automatically and successfully. This study that combines the image processing techniques with mini-Opto tomography imaging system ensured significant results in observing the tumoroid's growth rate and enlarging border over time, which is very critical to provide an emerging methodology in vitro cancer studies.
