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 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 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 Epigenetic Basis of Twin Discordance in Diseases: Future Benefits(2018) Demir, Ayşe Banu; Demir, NamıkMonozygotic twins share the same genotype since they are derived from the same zygote. However,monozygotic twin siblings frequently present many phenotypic differences, such as their susceptibilitiesto diseases. These isogenic individuals are not entirely identical. They exhibit phenotypic incompatibilityfor many features, from birth weight to complex diseases. Recently, several studies have been publishedshowing that phenotypic differences, especially in monozygotic twins, are being induced from prenatalperiod to life-long epigenetic differences. Epigenetic studies on twins have a great potential to contributeto our understanding of complex diseases, such as cancer, autoimmune disorders, psychiatric disordersand neurological diseases. Since monozygotic twins are genetic clones (genetically identical), they areconsidered as perfect models for studying the role of environmental factors as determinants of complexdiseases and phenotypes. In this review, a number of intrauterine effects and genetic mechanisms thatmay affect phenotypic, genotypic, and epigenetic differences between monozygotic twins were describedand effects of epigenetic mechanisms on complex diseases were mentioned. Further work on epigeneticchanges in diseases using incompatible monozygotic twin models, would lead to new developments inmedical therapies.Other Evaluation of Jak/Stat Signaling Pathway-Associated Protein Expression at Implantation Period: an Immunohistochemical Study in Rats(2023-10-20) Gürel, Çevik; Kuşçu, Gökçe Ceren; Vatansever, H. Seda; Köse, Can; İnan, Sevinç; Özbilgin, Kemal; Kırmaz, Cengiz; Vatansever, SedaObjective: The implantation period of gestation is a complex process in which numerous molecular pathways play a role. The Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway is one of the evolutionarily conserved cascades used to transduce a multitude signals for several biological events such as implantation and uterine receptivity. Previous studies have indicated that the implantation process is disrupted by the lack of proteins involved in this pathway. However, our literature knowledge showed that there is no study evaluated the expression of JAK/STAT signaling pathwayassociated proteins during the implantation period. This study investigated the expression patterns of JAK/STAT signaling pathway-associated proteins in rats by immunohistochemical (IHC) staining according to gestational days. Methods: In this study, thirty Wistar Albino rats weighing 250-300 g, without any problems in their menstrual cycles, were used. The pregnant animals were sacrificed on the 4th, 5th, and 6th days and histochemical and IHC analysis were performed on the uterine tissues taken from these animals. Results: In this study, protein expression of JAK1, JAK2, JAK3, STAT2, STAT3, STAT4, STAT5, and STAT6 belonging to the JAK/STAT pathway was evaluated in the uterine surface epithelium, gland structures, antimesometrial region, cells of the immune system, myometrium, mesometrial region and decidual cells, which are associated with the implantation process. The result of this evaluation reveals that the expression levels of these proteins in the JAK/STAT pathway vary in different days of the implantation period in implantation-related structures. Conclusion: This study indicates that JAK/STAT signaling pathway-associated proteins can function actively in the regulation of the immunological response of the uterus and embryo-uterus interaction during the implantation period in rats. However, the findings obtained from advanced research on JAK/STAT pathway can be used for treating recurrent pregnancy failures and in enhancing assisted reproductive technology.Article Is Human Vomeronasal Organ a Myth or a Neglected Structure?(2022-06-13) Fırat, Ayşegül; Hayran, Mürvet; Celebi, Ozlem OnerciThe human vomeronasal organ (VNO) is a structure situated under the anteroinferior side of the nasal septum. It is mainly described in the rodents and found as a part of the accessory olfactory system. It has been shown to consist of specialized olfactory sensory cells, which function in perception of pheromones. With a large number of literature on the human VNO, there is little concensus of its persistence and functionality in human. During a routine dissection of nasal cavity, we recognized a one-sided vomeronasal pit in one of the six fresh-frozen cadavers (17 %) and described the position and structure of this rare structure morphologically. The present study summarizes the literature about the VNO and describes its structural and functional findings.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.