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Öğe Chemical Composition, Radical Scavenging and Antimicrobial Activity of the Essential Oils of Thymus boveii and Thymus hyemalis(ACG PUBLICATIONS, 2011) Tepe, Bektas; Sarikurkcu, Cengiz; Berk, Seyda; Alim, Ahmet; Akpulat, H. AskinThis study was designed to examine the in vitro antimicrobial and antioxidant activities of the essential oil of T. boveii and T. hyemalis. According to the results of GC-EIMS analysis, essential oils were found rich in phenols and hydrocarbons. p-cymene, thymol and carvacrol were mainly found as the major compounds for the essential oils. Both plant species showed remarkable antioxidant activity in all test systems except chelating effect. In the case of antimicrobial activity, the oils showed remarkable growth inhibition against the tested microorganism except K. pneumoniae, P. aeruginosa, L. monocytogenes, P. fluorescens.Öğe Comprehensive bibliometric analysis and perspectives on therapies targeting colon cancer stem cells over a 40-year period(Elsevier, 2025) Berk, SeydaThe presence of cancer stem cells (CSCs) is one of the primary causes of recurring therapy resistance because they have two main capacities: self-renewal and avoiding apoptotic pathways. Despite their relevance, no full bibliometric analysis has yet been done in this topic. The goal of this work is to use bibliometric analysis to map the fundamental and emergent areas in therapeutics targeting colon cancer stem cells. To perform bibliometric analysis on colon cancer stem cells (CCSCs) literature, spanning roughly the last 40 years, in order to establish a firm base for future projections by emphasizing the findings of the most notable research. All information pertinent to CCSCs was accessed from Web of Science Core Collection database. In order to identify and analyze the research hotspots and trends related to this topic, Biblioshiny (RStudio) and VOSviewer were utilized to ascertain the countries/regions, institutions, journals, authors, references, and keywords involved. The targeted time span covered 1735 research-, and review articles. The most frequent keywords were colorectal cancer, cancer stem cells, and colon cancer, while the most trending keywords in the last few years were protein stability, spheroid formation, ubiquitination, exosomes, patient-derived organoids, and gut microbiota. Over the past 40 years, there has been a significant advancement in researchers' understanding of colon cancer stem cells. In addition, the cluster map of co-cited literature showed that colon cancer stem cell research has emerged as a research hotspot. It was also anticipated that the main focus of the future efforts appears to involve clinical applications of cell-targeted colon cancer therapy. These results provide researchers with a comprehensive understanding of this field and provide insightful ideas for further research. (c) 2025 The Author(s). Published by Elsevier BV on behalf of The Japanese Society for Regenerative Medicine. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/ licenses/by-nc-nd/4.0/).Öğe Evaluation and normalization of a set of reliable reference genes for quantitative sgk-1 gene expression analysis in Caenorhabditis elegans-focused cancer research(Taylor & Francis Inc, 2024) Ozdemir, Ozguer Ulkue; Yurt, Kubra; Pektas, Ayse Nur; Berk, SeydaMultiple signaling pathways have been discovered to play a role in aging and longevity, including the insulin/IGF-1 signaling system, AMPK pathway, TOR signaling, JNK pathway, and germline signaling. Mammalian serum and glucocorticoid-inducible kinase 1 (sgk-1), which has been associated with various disorders including hypertension, obesity, and tumor growth, limits survival in C. elegans by reducing DAF-16/FoxO activity while suppressing FoxO3 activity in human cell culture. C. elegans provides significant protection for a number of genes associated with human cancer. The best known of these are the lin-35/pRb (mammalian ortholog pRb) and CEP-1 (mammalian ortholog p53) genes. Therefore, in this study, we aimed to investigate the expression analyzes of sgk-1, which is overexpressed in many types of mammalian cancer, in mutant lin-35 and to demonstrate the validation of reference genes in wild-type N2 and mutant lin-35 for C. elegans-focused cancer research. To develop functional genomic studies in C. elegans, we evaluated the expression stability of five candidate reference genes (act-1, ama-1, cdc-42, pmp-3, iscu-1) by quantitative real-time PCR using five algorithms (geNorm, NormFinder, Delta Ct method, BestKeeper, RefFinder) in N2 and lin-35 worms. According to our findings, act-1 and cdc-42 were effective in accurately normalizing the levels of gene expression in N2 and lin-35. act-1 and cdc-42 also displayed the most consistent expression patterns, therefore they were utilized to standardize expression level of sgk-1. Furthermore, our results clearly showed that sgk-1 was upregulated in lin-35 worms compared to N2 worms. Our results highlight the importance of definitive validation using mostly expressed reference genes.Öğe In vitro amoebicidal activities of Teucrium polium and T. chamaedrys on Acanthamoeba castellanii trophozoites and cysts(SPRINGER, 2012) Tepe, Bektas; Malatyali, Erdogan; Degerli, Serpil; Berk, SeydaAmoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Teucrium polium and Teucrium chamaedrys. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellani trophozoites and cysts were decreased during the experimental process. Both extracts showed time- and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, T. chamaedrys showed the strongest amoebicidal effect on the trophozoites. In the presence of 16 mg/ml or above extract concentrations, no viable trophozoites were observed within 48 h. In the case of T. polium, no viable trophozoites were observed within 48 h at 32 mg/ml concentration. As expected, cysts were found more resistant to the extracts than the trophozoites.Öğe In vitro amoebicidal activity of four Peucedanum species on Acanthamoeba castellanii cysts and trophozoites(SPRINGER, 2012) Malatyali, Erdogan; Tepe, Bektas; Degerli, Serpil; Berk, Seyda; Akpulat, H. AskinAmoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which is less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Peucedanum caucasicum, Peucedanum palimbioides, Peucedanum chryseum, and Peucedanum longibracteolatum, which are endemic in Turkish flora except P. caucasicum. Extracts were evaluated for their amoebicidal activities using an inverted light microscope. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellani trophozoites and cysts were determined during the experimental process (72nd hour). All of the extracts showed a time and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, P. longibracteolatum showed the strongest amoebicidal effect on the trophozoites and cysts. In the case of 32 mg/ml concentration of extract, no viable trophozoites or cysts were determined between 24th and 72nd hour. Similar results were obtained from the extract at 16.0 mg/ml concentration against trophozoites. At this concentration value, number of viable cysts was determined as 10.6 +/- 2.1 in the 24th hour. trophozoites were determined in the 48th hour. At the same concentration, 51% of the cysts were killed by the extract in the 72nd hour. As expected, cysts were found more resistant to the extracts than the trophozoites.Öğe In vitro amoebicidal activity of Origanum syriacum and Origanum laevigatum on Acanthamoeba castellanii cysts and trophozoites(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2012) Degerli, Serpil; Tepe, Bektas; Celiksoz, Ali; Berk, Seyda; Malatyali, ErdoganIn some patients, complete treatment of amoebic keratitis is difficult because of the resistance of cysts to therapeutic agents. The aim of this study was to evaluate the in vitro amoebicidal activity of methanolic extracts of Origanum syriacum and Origanum laevigatum. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased. Both extracts showed a time and dose dependent amoebicidal action on the trophozoites and cysts. Of the extracts tested, O. syriacum showed the stronger amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within third hour. The extract was also found effective against the cysts within 24th hour. In the case of O. laevigatum, no viable trophozoites were observed within 72nd hour at the concentrations of 16 and 32 mg/ml. As expected, cysts were found more resistant to the extracts than the trophozoites. (C) 2012 Elsevier Inc. All rights reserved.Öğe Insulin and IGF-1 extend the lifespan of Caenorhabditis elegans by inhibiting insulin/insulin-like signaling and mTOR signaling pathways: C. elegans - Focused cancer research(Academic Press Inc Elsevier Science, 2024) Berk, SeydaThe mutations in Caenorhabditis elegans (C. elegans) that extend lifespan slow down aging by interfering with several signaling pathways, including the insulin/IGF-1 signaling (IIS) pathway, AMP-activated protein kinase (AMPK), and mechanistic target of rapamycin (mTOR). The tumor suppressor pRb (retinoblastoma protein) is believed to be involved in almost all human cancers. Lin-35, the C. elegans orthologue of the tumor suppressor pRb, was included in the study to explore the effects of insulin and IGF-1 because it has been linked to cancerrelated pRb function in mammals and exhibits a tumor suppressor effect by inhibiting mTOR or IIS signaling. According to our results, IGF-1 or insulin increased the lifespan of lin-35 worms compared to N2 worms by increasing fertilization efficiency, also causing a significant increase in body size. It was concluded that the expression of daf-2 and rsks-1 decreased after insulin or IGF-1 administration, thus extending the lifespan of C. elegans lin-35 worms through both IIS and mTOR-dependent mechanisms. This suggests that it was mediated by the combined effect of the TOR and IIS pathways. These results, especially obtained in cancer-associated mutant lin-35 worms, will be useful in elucidating the C. elegans cancer model in the future.Öğe Lifespan extension with mTOR inhibitors rapamycin, everolimus, and temsirolimus in Caenorhabditis elegans (Maupas, 1899)(Russian Acad Sci, Inst Parasitology, 2024) Demirel, Tugba; Ozdemir, Ozgur Ulku; Berk, SeydaA master regulator of longevity in all eukaryotes, the mechanistic target of rapamycin signalling pathway (mTOR) is thought to mediate certain effects of dietary restriction. The tumour suppressor pRb , whose orthologue in Caenorhabditis elegans is lin-35/pRb , is predicted to be involved in almost all human cancers. As lin-35 is linked to cancer -associated pRb function in mammals and also has a tumour suppressor effect by inhibiting mTOR signalling, the lin-35 was included in the study to investigate the effects of mTOR inhibitors. We showed that mTOR inhibitors extended the lifespan of N2 and lin-35 C. elegans by reducing fertilisation efficiency and resulted in reductions in the body size of worms. Additionally, rsks-1/S6K and let-363/TOR expressions increased in the presence of rapamycin, temsirolimus, or everolimus. The elucidation of molecular mechanisms of rapamycin and its analogues regulating health prolonging will expand their therapeutic applicability in treatment of human aging and age -related disorders.Öğe Screening of the antioxidant, antimicrobial and DNA damage protection potentials of the aqueous extract of Asplenium ceterach DC(ACADEMIC JOURNALS, 2011) Berk, Seyda; Tepe, Bektas; Arslan, Serdal; Sarikurkcu, CengizIn this study, in vitro antioxidant, antimicrobial and DNA damage protection potentials of the aqueous extract of Asplenium ceterach was firstly evaluated in addition to its total phenolic and flavonoid contents. Antioxidant activity was determined by five complementary test systems named beta-carotene/linoleic acid, 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging, reducing power, chelating effect and phosphomolibdenum methods. Except for chelating effect assay, the extract exhibited remarkable activity potential. Antimicrobial activity was determined by agar-well diffusion and minimum inhibitory concentration tests. In this case, Shigella dysenteriae and Staphylococcus aureus were found to be the most sensitive microorganisms. According to the electrophoretic pattern of pBR322 plasmid DNA after treatment with UV and H2O2, supercoiled DNA was successfully protected in the presence of 20 mg/ml or above concentrations of aqueous extract.Öğe Screening of the antioxidant, antimicrobial and DNA damage protection potentials of the aqueous extract of inula oculus-christi(2011) Berk, Seyda; Tepe, Bektas; Arslan, SerdalIn this study, in vitro antioxidant, antimicrobial and DNA damage protection potentials of the aqueous extract of Inula oculus-christi was firstly evaluated in addition to its total phenolic and flavonoid contents. Antioxidant activity was determined by five complementary test systems named as ?-carotene linoleic acid, 2,2-diphenyl-1-picrylhydrazyl free radical (DPPH) free radical scavenging, reducing power, chelating effect and phosphomolibdenum methods. The extract exhibited remarkable activity potential in DPPH free radical scavenging system. Antimicrobial activity was determined by agar-well diffusion and minimum inhibitory concentration tests. In this case, Shigella dysanteriae, Staphylococcus aureus, Shigella boydii and Bacillus subtilis was found as the sensitive microorganisms. According to the electrophoretic pattern of pBR322 plasmid DNA after treatment with UV and H2O2, supercoiled DNA was successfully protected in the presence of 14.28 mg/ml or above the concentrations of the aqueous extract. ©2011 Academic Journals.Öğe Screening of the antioxidant, antimicrobial and DNA damage protection potentials of the aqueous extract of Inula oculus-christi(ACADEMIC JOURNALS, 2011) Berk, Seyda; Tepe, Bektas; Arslan, SerdalIn this study, in vitro antioxidant, antimicrobial and DNA damage protection potentials of the aqueous extract of Inula oculus-christi was firstly evaluated in addition to its total phenolic and flavonoid contents. Antioxidant activity was determined by five complementary test systems named as beta-carotene linoleic acid, 2,2-diphenyl-1-picrylhydrazyl free radical (DPPH) free radical scavenging, reducing power, chelating effect and phosphomolibdenum methods. The extract exhibited remarkable activity potential in DPPH free radical scavenging system. Antimicrobial activity was determined by agar-well diffusion and minimum inhibitory concentration tests. In this case, Shigella dysanteriae, Staphylococcus aureus, Shigella boydii and Bacillus subtilis was found as the sensitive microorganisms. According to the electrophoretic pattern of pBR322 plasmid DNA after treatment with UV and H2O2, supercoiled DNA was successfully protected in the presence of 14.28 mg/ml or above the concentrations of the aqueous extract.Öğe Screening of the in vitro amoebicidal activities of Pastinaca armenea (Fisch & CAMey.) and Inula oculus-christi (L.) on Acanthamoeba castellanii cysts and trophozoites(SPRINGER, 2012) Degerli, Serpil; Berk, Seyda; Malatyali, Erdogan; Tepe, BektasThe aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of Pastinaca armenea and Inula oculus-christi from Turkey. In the presence of aqueous extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time- and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, I. oculus showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32.00 mg/ml extract solution in the media, no viable trophozoites were determined from the time of 24 h. Moreover, in the presence of 16.00 mg/ml I. oculus-christi extract, no viable trophozoites were detected in 72 h of the experiment. Effectiveness of I. oculus-christi extract was found moderate against the cysts. In the presence of 32.00 mg/ml extract, only 25.3% of the total cysts were killed effectively. In the case of P. armenea, 40.3% and 23.0% of the trophozoites and cysts were killed in the presence of 32.00 mg/ml extract at the end of the experimental process (72 h), respectively.Öğe The combination of metformin and high glucose increased longevity of Caenorhabditis elegans a DAF-16/FOXO-independent manner: cancer/diabetic model via C. elegans(Frontiers Media Sa, 2024) Berk, Seyda; Cetin, Ali; Ozdemir, Ozgur Ulkue; Pektas, Ayse Nur; Yurtcu, Nazan; Dastan, Sevgi DurnaIntroduction Sedentary lifestyles and diets with high glycemic indexes are considered to be contributing factors to the development of obesity, type 2 diabetes in humans. Metformin, a biguanide medication commonly used to treat type 2 diabetes, has been observed to be associated with longevity; however, the molecular mechanisms underlying this observation are still unknown.Methods The effects of metformin and high glucose, which have important roles in aging-related disease such as diabetes and cancer, were studied in lin-35 worms because they are associated with cancer-associated pRb function in mammals and have a tumour suppressor property.Results and Discussion According to our results, the negative effect of high glucose on egg production of lin-35 worms was greater than that of N2 worms. High glucose shortened lifespan and increased body length and width in individuals of both strains. Metformin treatment alone extended the lifespan of N2 and lin-35 worms by reducing fertilization efficiency. However, when metformin was administered in the presence of high glucose, the lifespan of lin-35 worms was clearly longer compared to N2 worms. Additionally, we conclude that glucose and metformin in lin35 worms can extend life expectancy through a DAF-16/FOXO-independent mechanism. Furthermore, the results of this study will provide a new perspective on extending mammalian lifespan through the model organism C. elegans.
