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 Bioinformatics Based Drug Repurposing Approach for Breast and Gynecological Cancers: RECQL4/FAM13C Genes Address Common Hub Genes and Drugs(Galenos Publ House, 2025-01-02) Duran, Gizem Ayna; Duran, Assist. Prof. Dr. Gizem AynaObjective: The prevalence of breast cancer and gynaecological cancers is high, and these cancer types can occur consecutively as secondary cancers. The aim of our study is to determine the genes commonly expressed in these cancers and to identify the common hub genes and drug components. Materials and Methods: Gene intensity values of breast cancer, gynaecological cancers such as cervical, ovarian and endometrial cancers were used from the Gene Expression Omnibus database Affymetrix Human Genome U133 Plus 2.0 Array project. Using the linear modelling method included in the R LIMMA package, genes that differ between healthy individuals and cancer patients were identified. Hub genes were determined using cytoHubba in Cytoscape program. “ShinyGo 0.80” tool was used to determine the disease-specific biological KEGG pathways. Drug.MATADOR from the ShinyGo 0.80 tool was used to predict drug-target relationships. Results: The RecQ Like Helicase 4 and Family with Sequence Similarity 13 Member C genes were found to be similarly expressed in breast cancer and gynaecological cancers. Upon KEGG pathway analyses with hub genes, Drug.MATADOR analysis with hub genes related to cancer related pathways was performed. We have determined these gene/drug interactions: NBN (targeted by Hydroxyurea), EP300 (targeted by Acetylcarnitine) and MAPK14 (targeted by Salicylate and Dibutyryl cyclic AMP). Conclusion: The drugs associated with hub genes determined in our study are not routinely used in cancer treatment. Our study offers the opportunity to identify the target genes of drugs used in breast and gynaecological cancers with the drug repurposing approach.Article Fluorescence Microscopy Denoizing Via Neighbor Linear Embedding(Istanbul University, 2024-01-31) Kırmızıay, Çağatay; Aydeniz, Burhan; Türkan, MehmetOne of the difficulties in studying fluorescence imaging of biological structures is the presence of noise corruption. Even though hardware- and software-related technologies have undergone continual improvement, the unavoidable effect of Poisson–Gaussian mixture type is generally encountered in fluorescence microscopy images. This noise should be mitigated to allow the extraction of valuable information from fluorescence images for various types of biological analysis. Thus, this study introduces a new and efficient learning-based denoizing approach for fluorescence microscopy. The proposed approach is based mainly on linear transformations between noise-free and noisy submanifold structures of patch spaces, benefiting from linear neighbor embeddings of local image patches. According to visual and statistical results, the developed algorithm called "neighbor linear-embedding denoizing" algorithm has a highly competitive and generally superior performance in comparison with the other algorithms used for fluorescence microscopy image denoizing in the literature. © 2024 Istanbul University. All rights reserved.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 Preantral Follicle Morphometry and Ultrastructure of Antral Follicles in Anatolian Water Buffalo(TUBITAK, 2023-10-17) Bakı, Acar, D.; Bırdane, M.K.; Tokyol, Ç.; Göçmen, Karabekır, N.N.; Hayran, Mürvet; Özenç, E.; Aktepe, F.; Uçar, Mehmet; Hayran, Hatice Mürvet; Göçmen Karabekır, Nermin Nüket; Bakı Acar, Duygu; Karabekir, Nermin Nuket Gocmen; Yağcı, İlknur Pir; Yazıcı, Ebubekir; Mas, Nuket Gocmen; Acar, Duygu BakiThis study aimed to evaluate quantitative and morphometric analyses of preantral follicles and the ultrastructural characteristics of antral follicles in different oestrous cycle stages in Anatolian water buffaloes. Twenty-four ovaries collected from twelve slaughtered Anatolian water buffaloes were classified macroscopically as luteal or follicular stages. The ovaries were prepared for histological examination (Hematoxylin-eosin staining), and primordial, primary, and secondary follicle numbers were calculated, and the diameters of oocytes, follicles, and nuclei were measured under a light microscope with a micrometre. The theca and granulosa cells of antral follicles were observed under a transmission electron microscope. The mean number of preantral follicles was 18584 ± 4855, and there was a significant difference in the number of primordial follicles (p < 0.0001) and primary follicles (p < 0.001) between buffaloes. The number of primordial follicles was 10,636, that of primary follicles was 6514, and that of secondary follicles was 1434; the statistical difference was found between primordial, primary, and secondary follicle and oocyte diameters (p < 0.001) in Anatolian water buffaloes. In this study, the ultrastructural evaluation of antral follicles showed that the theca cells were active in the luteal stage with their functional organelles and higher lipid droplets. The granulosa cells were still inactive in the luteal stage. In the follicular stage of the oestrous cycle, the theca cells were found inactive, although granulosa cells showed moderate or high activity. It was found that the serum progesterone concentration and cycle stage directly affected the theca and granulosa cell ultrastructural activity in Anatolian water buffalo. In this research, information from light and electron microscopic analyses of preantral and antral follicles has been obtained for the first time for Anatolian water buffaloes. The result of our study suggests that detailed molecular research is needed to evaluate the ultrastructural activity of antral follicles in different oestrous cycle stages and steroidogenic circumstances. © TÜBİTAK.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 Citation - WoS: 2Citation - Scopus: 2Testing the Concealed Ovulation Hypothesis in the Framework of Facial Symmetry Fluctuations Moderated by Menstrual Cycle in Women(Turkish Psychologists Assoc, 2010) Çeti̇nkaya, Hakan; Dural, Seda; Gulbetekin, Evrim; Çetinkaya, Seda DuralWith three studies, a long lived position that women have concealed ovulation, and its possible adaptive value were investigated. In the first study, systematic changes in women across the menstural cycle were elaborated and of those, cyclic changes in the facial symmetry in regularly ovulating women were investigated. The findings showed predictable fluctuations on females' facial symmetry throughout their menstural phases. In order to determine whether the differences among the deviation from the symmetry scores of the facial pictures obtained from four menstural phases (namely, menstural, proliferative, ovulatory, and secretory phases) were detectable by males, in the second experiment, males evaluated the facial-menstural pictures for their attractiveness. The male participants rated the pictures obtained from ovulatory phases as the most attractive of all. Also they found the pictures obtained from the menstural phases to be least attractive. In the third study, half of the male participants (familiar males) rated four menstural pictures obtained from the same females, the other half of them (unfamiliar males) rated four menstural pictures, but this time each of which obtained from different females. The males in the latter group were not able to distinguish attractiveness of the facial pictures of different females. The results indicate that although there is some extent of concealment of ovulation in women as an adaptation, it is not completely concealed, especially from the familiar (or pair-bonded) males. Thus, men might have equipped with a counter-adapt, a mental device, through their evolutionary history to cope with the problem of concealment of ovulation in women by staying with her and observing the cyclic changes on her facial attractiveness.Article Citation - WoS: 9Citation - Scopus: 9Classical Heart Rate Variability and Non-Linear Heart Rate Analysis in Mice Under Na-Pentobarbital and Ketamine/Xylazine Anesthesia(Tubitak Scientific & Technical Research Council Turkey, 2022-01-01) Kazdagli, Hasan; Ozel, Hasan Fehmi; Ozbek, Mustafa; Alpay, Suheda; Alenbey, MuruvvetBackground/aim: Anesthetics are often used in animal experiments to achieve immobilization and relieve pain. However, many anesthetics can alter the dynamics of cardiovascular systems. We aimed to compare the effects of two frequently used anesthetics agents on heart rate variability (HRV) parameters in mice. Materials and methods: This observational study was performed between May and June 2014 in 21 male BALB/c mice aged 16-20 weeks. The animals were divided into three groups: pentobarbital (P), (n = 7); pentobarbital+fentanyl (P+ F), (n = 7); and ketamine+xylazine (K+X), (n = 7). Surface electrocardiography (ECG) electrodes were placed in lead II configuration. 'the tachogram of RR intervals was obtained after R waves were detected using the Pan-Tompkins real-time QRS recognition algorithm. Frequency-domain, time-domain, and nonlinear HRV analyses were performed. Results: The bradycardia effect was higher in the K+X group (p < 0.01). Time-domain indices were higher in group K+X compared to group P (p < 0.01) and group P+F (p < 0.001). Very low frequency (VLF) power was significantly lower in group K+X compared to group P and group P+F (p < 0.01). Low frequency (LF) power, low frequency/high frequency (LF/HF) ratio, and total power (TP) were higher in group K+X compared to group P (p < 0.01) and group P+F (p < 0.001). The detrended fluctuation analysis short-term parameter (DFA alpha(1)) was significantly higher in group K+X compared to group P+F (p < 0.05) and the long-term parameter (DFA alpha(2)) was lower in group K+X compared to group P (p < 0.05). Standard deviations SD1 and SD2 were higher in group K+X compared to group P (p < 0.001) and group P+F (p < 0.001), SD2/SD1 ratio was lower in group K+X compared to group P (p < 0.05) and group P+F (p < 0.05). Entropy measures did not differ between groups. Conclusion: HRV analyses, including nonlinear methods, indicated that a K+X combination reduces imbalance and disorder in the regulation of the autonomic nervous system (ANS) in comparison to both P and the P+F combination.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.