TR Dizin İndeksli Yayınlar Koleksiyonu / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/4
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Article Porphyridium Cruentum as a Biological Component for the Green Synthesis of Metal Nanoparticles and for the Evaluation of Their Antimicrobial Activity(Field Crops Central Research Institute, 2025-08-21) Mutaf, Tugce; Çalışkan, Gülizar; Oncel, Suphi; Elibol, Murat; Mutaf-Kilic, TugceSilver nanoparticles are an alternative to new-generation antimicrobial agents with their antimicrobial activity. Iron and zinc nanoparticles can potentially be used as UV protection in various applications. Nowadays, green synthesis of nanoparticles as a sustainable alternative attracts attention. Microalgae are promising in nanoparticle synthesis among biological sources due to their high biomass productivity and heavy metal accumulation ability. The present study aimed to investigate the potential of synthesizing intracellular silver, zinc and iron nanoparticles from Porphyridium cruentum microalgae. For nanoparticle synthesis, the effects of metal solution concentration and amount of biomass on particle size were investigated. The nanoparticles were characterized by dynamic light scattering, UV-vis spectrophotometry, and antimicrobial activity test. Silver nanoparticles of 169.7 nm, zinc nanoparticles of 189 nm, and iron nanoparticles of 356.7 nm were characterized by DLS. 169.7 nm silver nanoparticles were synthesized with 9.83 mM AgNO3 concentration and 0.19 mg/ml biomass: metal solution mixing ratio. The surface plasmon resonance band of silver nanoparticles was observed in the 300-350 nm wavelength range. According to the antibacterial activity results of silver nanoparticles, inhibition zone diameters were obtained as 10.83±0.76 mm and 11.33±0.57 mm against Escherichia coli and Staphylococcus aureus bacteria, respectively.Article Upregulated Acute Systemic Inflammation-Related Genes Based on Endotoxin Exposure Provide ‘Survival Benefit’ or Create ‘High Risk of Death’ in Leukaemia and Colon Cancer(Istanbul University, 2024-07-10) Duran, Gizem Ayna; Duran, Assist. Prof. Dr. Gizem Ayna; Ayna Duran, GizemObjective: Although endotoxin exposure has been shown to trigger innate immune responses and promote cancer, it has also been shown to prevent cancer formation. In our study, survival analysis was performed to determine whether the upregulated genes triggered by endotoxins have hazardous effects on cancers or provide a survival benefit. Materials and Methods: Gene intensity values of control and bacterial endotoxin-administered individuals were obtained from the Gene Expression Omnibus database. Using the R "Linear Models for Microarray Data" package, differentially expressed gene analyses were conducted to determine genes that differ between healthy and bacterial endotoxin-administered samples. "ShinyGo 0.80" web-based tool was used to determine the disease types indicated by these genes. The "Kaplan-Meier Plotter" web-based tool was used to conduct survival analysis. Results: Genes that create an innate immune response to bacterial endotoxin exposure and are upregulated differently than in individuals without exposure were identified. According to gene enrichment analyses, the two main types of cancer identified were leukaemia/lymoma and colon cancer. We detected that MLF1, STAT5B, and BCL3 genes led to poor survival; however, the ARHGAP26 gene was protective for acute myeloid leukaemia patients. In the case of colon cancer, SMAD7 and TLR2 genes were determined as leading to "high risk of death". Conclusion: Once the systemic inflammation-related genes identified in our study are confirmed through laboratory experiments in samples taken from solid tissue in the case of colon cancer and at the level of genes obtained from blood samples in leukemias, genetically targeted treatments will also be possible.Article Identification of the Role of Tg2 on the Expression of Tgf-Β, Timp-1 and Timp-2 in Aged Skin(Walter De Gruyter Gmbh, 2024-02-12) Ergülen, Elvan; Akdoğan, Gül; Guner, Gul AkdoganObjectives Transglutaminase 2 (TG2) is a unique protein having enzymatic and nonenzymatic functions that have been implicated in various biological and pathological processes such as cell survival and apoptosis, cell signaling, differentiation, adhesion and migration, wound healing and inflammation. As reported in previous studies, TG2 expression and activity increase by age suggesting that TG2 possibly has roles in cellular aging process. In this study, we aimed to explore the role of TG2 in chronological skin aging through its impact on the expression of some important extracellular matrix (ECM) proteins including TGF-beta, TIMP-1 and TIMP-2. Methods We have compared TG2 expression and activity in young and in vitro chronologically aged human dermal fibroblasts via Western blot and in situ TG2 activity assays. Afterwards, we inhibited TG2 expression via siRNA transfection and activity via active site inhibitor of TG2 separately in aged dermal fibroblasts and monitored the expression levels of TGF-beta, TIMP-1 and TIMP-2 in these cells by Western blot and compared to that of untreated control cells. Results We obtained evidence that both TG2 expression and activity increase in aged cells. However, protein levels of TGF-beta, TIMP-1 and TIMP-2 do not exhibit any significant difference in TG2 downregulated or TG2 activity inhibited aged cells compared to control cells. Conclusions Our results indicate that changes in the expression and activity of TG2 in (in vitro) chronologically aged human dermal fibroblasts do not impact the expression patterns of TGF-beta, TIMP-1 and TIMP-2 proteins.Article Classification of Colon Cancer Patients Into Consensus Molecular Subtypes Using Support Vector Machines(2023-12-28) Koçhan, Necla; Dayanç, Barış EmreBackground/aim: The molecular heterogeneity of colon cancer has made classification of tumors a requirement for effective treatment. One of the approaches for molecular subtyping of colon cancer patients is the consensus molecular subtypes (CMS), developed by the Colorectal Cancer Subtyping Consortium. CMS-specific RNA-Seq-dependent classification approaches are recent, with relatively low sensitivity and specificity. In this study, we aimed to classify patients into CMS groups using their RNA-seq profiles. Materials and methods: We first identified subtype-specific and survival-associated genes using the Fuzzy C-Means algorithm and log- rank test. We then classified patients using support vector machines with backward elimination methodology. Results: We optimized RNA-seq-based classification using 25 genes with a minimum classification error rate. In this study, we reported the classification performance using precision, sensitivity, specificity, false discovery rate, and balanced accuracy metrics. Conclusion: We present a gene list for colon cancer classification with minimum classification error rates and observed the lowest sensitivity but the highest specificity with CMS3-associated genes, which significantly differed due to the low number of patients in the clinic for this group.Article In Silico Approach for Identification of PI3K/MTOR Dual Inhibitors for Multiple Myeloma Treatment(Istanbul Univ, 2023-04-14) Masalaci, Ilke; Akdogan, Yaren; Mutlu, Ozge; Eyvaz, Hande; Kiraz, YagmurObjective: Multiple myeloma is a hematologic malignancy in which targeting phosphoinositide 3 kinase (PI3K) and/or the mammalian target of rapamycin (mTOR) individually has been shown to have anti-proliferative effects, however, inhibiting both proteins simultaneously has been reported to have more effective results for its treatment. The aim of this study is to determine the molecular interactions and predicted inhibitory effects of 40 different dual inhibitors on mTOR, PI3K delta, and PI3K gamma to propose potentially the most effective dual inhibitor that targets the PI3K delta and PI3K gamma isoforms as well as the mTOR proteins since those isoforms are known to be predominant in multiple myeloma patients. Therefore, the focus in this study is built around the specific targeting of the PI3K delta and PI3K gamma isoforms from the multiple myeloma perspective. Materials and Methods: In silico docking experiments were conducted to determine the binding energies for different ligands that target mTOR, PI3K delta, and PI3K gamma. Protein-dual inhibitor complexes and the amino acids and bond types were visualized to identify molecular interactions. The absorption, distribution, metabolism, and excretion properties of dual inhibitors were analyzed and evaluated. Results: The binding affinity values were found to be between -7 and -9.9 kcal/mol. The toxicity prediction values of the selected dual inhibitors were obtained from the Pro-Tox-II web tool and classified according to the globally harmonized system of classification of labeling of chemicals. Conclusion: Correspondingly, among all dual inhibitors, Vistusertib is determined to be a promising compound against multiple myeloma cells by inhibiting both PI3K delta and PI3K gamma as well as mTORC1/2.Article Turkish Adaptation and Validation of Behavioral Inhibition Questionnaire Parent Form(Aves, 2023-01-02) Kilinc, Saliha; Bilgiç, Ayhan; Gormez, VahdetBackground: Behavioral inhibition has been proposed as a temperamental risk factor for the development of childhood anxiety disorders universally; however, there is no validated instrument for, especially, its evaluation in Turkish children. This study aimed to examine reliability and validity of the Turkish version of Behavioral Inhibition Questionnaire parent form for children aged 3-7 years. Methods: Around 250 mothers or fathers of 3-7 years old children were recruited from non-clinical population to collect responses to the questionnaires. The sample was created by reaching 3 schools at preschool or elementary grade for the purpose of providing the questionnaires filled about the student and/or his/her little sisters and brothers by their parents; questionnaires were sent out to parents and then gathered. Parents were asked to fill sociodemographic data form, Behavioral Inhibition Questionnaire parent form, Children Behavior Questionnaire, and Strengths and Difficulties Questionaire parent form in order to perform convergent and divergent validity analyses. Results: As a result of reliability analysis, total Cronbach alpha coefficient for Behavioral Inhibition Questionnaire was determined as 0.92 with strong reliability. The internal consistency coefficients for Behavioral Inhibition Questionnaire subscales also showed strong reliability with alphas ranging between 0.81 and 0.87 except for the performance (a = 0.69) and physical challenges (a = 0.19) subscales of which some items were excluded due to item-total correlations and confirmatory factor analysis results. In the validity assessment analyses, confirmatory factor analysis demonstrated that Behavioral Inhibition Questionnaire has a construct validity with 5 factors loaded on the 2-second order main factors and one third-order final factor (root mean square error = 0.032, root mean square residual = 0.153, Comparative Fit Index = 0.978, Goodness of Fit Index = 0.915, and Turker-Lewis Index = 0.970). While the strongest correlations with the overall Behavioral Inhibition Questionnaire score were found for 2 main subscales, inhibition to social novelties (r = 0.926, P <.001) and situational novelties (r = 0.928, P <.001), similarly peers (r = 0.848, P <.001) and new situations (r = 0.898, P <.001) subscales, had strong correlations with the overall Behavioral Inhibition Questionnaire score. The weakest correlation with overall Behavioral Inhibition Questionnaire score was observed for physical challenges subscale even though this subscale displayed moderate association (r = 0.454, P <.001). A good convergent validity was determined accompanied by significant moderate positive correlations with Children Behavior Questionnaire shyness and Strengths and Difficulties Questionnaire internalizing scales. An adequate divergent validity was also demonstrated based on significant positive mild to moderate correlations with Children Behavior Questionnaire impulsivity, Children Behavior Questionnaire smiling/laugh, Strengths and Difficulties Questionnaire prosocial scales, and nonsignificant correlation with Strengths and Difficulties Questionnaire externalizing scale. Conclusion: The study demonstrated that the Turkish version of the Behavioral Inhibition Questionnaire parent form is an effective tool with good reliability and validity among 3-7 years old children.Article Citation - WoS: 3Citation - Scopus: 3A Minimally Invasive Transfer Method of Mesenchymal Stem Cells To the Intact Periodontal Ligament of Rat Teeth: a Preliminary Study(Tubitak Scientific & Technical Research Council Turkey, 2018-10-25) Gul Amuk, Nisa; Kurt, Gokmen; Kartal Yandim, Melis; Adan, Aysun; Baran, Yusuf; Amuk, Nisa Gul; Yandım, Melis KartalThe aim of this study was to introduce a minimally invasive procedure for mesenchymal stem cell (MSC) transfer into the intact periodontal ligament (PDL) of the molar teeth in rats. Ten 12-week-old Wistar albino rats were used for this preliminary study. MSCs were obtained from bones of two animals and were labeled with green fluorescent protein (GFP). Four animals were randomly selected for MSC injection, while 4 animals served as a control group. Samples were prepared for histological analysis, Cox-2 mRNA expression polymerase chain reaction analysis, and fluorescent microscopy evaluation. The number of total cells, number of osteoclastic cells, and Cox-2 mRNA expression levels of the periodontal tissue of teeth were calculated. The number of total cells was increased with MSC injections in PDL significantly (P < 0.001). The number of osteoclastic cells and Cox-2 mRNA expression were found to be similar for the two groups. GFP-labeled MSCs were observed with an expected luminescence on the smear samples of the PDL with transferred MSCs. The results of this preliminary study demonstrate successful evidence of transferring MSCs to intact FIX in a nonsurgical way and offer a minimally invasive procedure for transfer of MSCs to periodontal tissues.Article Citation - WoS: 7Citation - Scopus: 11The Effect of Virtual Laboratory Simulations on Medical Laboratory Techniques Students' Knowledge and Vocational Laboratory Education(Walter De Gruyter Gmbh, 2022-08-01) Keles, Didem; Bulgurcu, Alihan; Demir, Esra Feyzioglu; Şemin, Makbule İlgi; Feyzioğlu Demir, Esra; Şemin, Ilgi Makbule; Feyzioğlu-demir, EsraObjectives Virtual laboratory simulations (VLSs) are computer-based tools that offer unlimited application options in scientific, medical, and engineering fields. The aim of this study was to evaluate whether VLSs are efficient learning tools and how these simulations can be integrated into laboratory practice in medical laboratory education. Methods In this pre-test/post-test control group study, 32 volunteers were randomly assigned to either experimental or control groups. The experimental group performed laboratory simulations based on biochemistry and microbiology and then completed a self-report survey to evaluate their satisfaction and beliefs about simulations. Results In the experimental group, post-test scores of each simulation were significantly elevated compared to pre-test scores; however, pre- and post-test scores of control group were statistically the same. The experimental group agreed that these simulations should be applied before theoretical lectures and laboratory practices. They also highlighted that translating from English to their native language creates difficulties in applying and understanding the simulation. Conclusions We emphasized that VLSs are excellent learning tools that increase not only the knowledge but also the self-motivation and focus of the students. Based on feedbacks, native language options are necessary to enable the students to achieve equality of opportunity in education.