Fen Edebiyat Fakültesi / Faculty of Letters and Science
Permanent URI for this collectionhttps://hdl.handle.net/11727/1396
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Item The Capacitance/Conductance And Surface State Intensity Characteristics Of The Al/(Cmat)/P-Si Structures(Başkent Üniversitesi Fen Edebiyat Fakültesi, 2024-02-01) Cetinkaya, H. G.; Bengi, S.; Sevgili, O.; Altindal, S.To determine the Al/(CMAT)/p-Si structure's admittance analysis, capacitance/conductance versus frequency (C/G-V-f) data was obtained in the 3 kHz-3 MHz and -2/4 V ranges at room temperature. The powder form of CeMgAl11O19: Tb (CMAT) was thermally evaporated onto the front of p-Si wafer at 10-6 Torr as interfacial layer. From the Nicollian and Brews method, voltage-dependent spectra of Rs were derived for various frequencies. The parallel conductance and low-high frequency capacitance (CLF-CHF) techniques, respectively, were used to determine the voltage and frequency dependent spectra of Nss and their lifetime (tau). Surface states (Nss), which are identified by admittance measurements, emerge at the M/S interlayer because of high capacitance and conductance values at low frequencies. This can also be explained by the Nss's ability to track ac signals well at lower frequencies. The normalized parallel conductance versus frequency (Gp/omega-f) plot under various biases shows a peak because of Nss existence. x-ray diffractometer (XRD) was used for structural investigation and the average crystal size (D) of the nanocrystals (CMAT) was found to be less than 0.34 nm by using the Debye-Scherer's equation.Item A Partial Epithelial-Mesenchymal Transition Signature For Highly Aggressive Colorectal Cancer Cells That Survive Under Nutrient Restriction(JOURNAL OF PATHOLOGY, 2024-01-24) Pastorino, Gil A.; Sheraj, Ilir; Oral, Goksu; Gulec Taskiran, Aliye Ezgi; Palmisano, Ralph; Schneider-Stock, ReginePartial epithelial-mesenchymal transition (p-EMT) has recently been identified as a hybrid state consisting of cells with both epithelial and mesenchymal characteristics and is associated with the migration, metastasis, and chemoresistance of cancer cells. Here, we describe the induction of p-EMT in starved colorectal cancer (CRC) cells and identify a p-EMT gene signature that can predict prognosis. Functional characterisation of starvation-induced p-EMT in HCT116, DLD1, and HT29 cells showed changes in proliferation, morphology, and drug sensitivity, supported by in vivo studies using the chorioallantoic membrane model. An EMT-specific quantitative polymerase chain reaction (qPCR) array was used to screen for deregulated genes, leading to the establishment of an in silico gene signature that was correlated with poor disease-free survival in CRC patients along with the CRC consensus molecular subtype CMS4. Among the significantly deregulated p-EMT genes, a triple-gene signature consisting of SERPINE1, SOX10, and epidermal growth factor receptor (EGFR) was identified. Starvation-induced p-EMT was characterised by increased migratory potential and chemoresistance, as well as E-cadherin processing and internalisation. Both gene signature and E-cadherin alterations could be reversed by the proteasomal inhibitor MG132. Spatially resolving EGFR expression with high-resolution immunofluorescence imaging identified a proliferation stop in starved CRC cells caused by EGFR internalisation. In conclusion, we have gained insight into a previously undiscovered EMT mechanism that may become relevant when tumour cells are under nutrient stress, as seen in early stages of metastasis. Targeting this process of tumour cell dissemination might help to prevent EMT and overcome drug resistance. (c) 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.Item Mass Migration Governance And Openness Toward Refugees: Comparing Germany And Turkey(INTERNATIONAL MIGRATION, 2024-01-22) Erden, Yigit; Ozcurumez, SaimeThis study seeks answers to the question: 'Under what conditions do communities with migration experience in refugee-receiving states become more open toward accepting more refugees and why?'. The research seeks answers to this question by examining the attitudes of individuals (N = 37) from Turkey who have been living in Germany for at least a year and who have sufficient familiarity with the characteristics of governance of mass migration in both countries. The findings suggest that the respondents are more pessimistic about the consequences of Turkey accepting more refugees in the future, while they are optimistic about the outcomes of the arrival of more refugees in Germany. This study posits that receiving communities' perceptions about the host state's regulatory and institutional capacity in managing mass migration and integration of refugees shape their attitudes toward the possibility of the influx of more refugees over time. The findings indicate that efficient mass migration governance in a receiving state is identified through four characteristics: (i) admission of educated refugees, (ii) proper refugee registration procedures, (iii) systematic integration processes, and (iv) effective monitoring and law enforcement mechanisms. The study concludes that local communities view public authorities as the key actors in managing the consequences of mass migration and establishing and sustaining good mass migration governance at the receiving state level is likely to facilitate positive attitudes towards accepting more refugees.Item Investigation Of Possible Use Of Pheromone Trap For Adult Population Development And Control Of Ips Sexdentatus (Börner, 1776) (Coleoptera: Scolytidae) Damaging Black Pine In Başkent University Bağlica Campus Afforestation Area(TURKIYE ENTOMOLOJI DERGISI-TURKISH JOURNAL OF ENTOMOLOGY, 2024-04-12) Erdogan, CemThe six -toothed pine bark beetle, Ips sexdentatus (Borner, 1776) (Coleoptera: Scolytidae), is one of the important pests of Pinus and Picea species in the forests of Turkiye. Baskent University Baglica Campus was established in 1993 and approximately 5 million trees have been planted in the area to date, including those that have dried up. Pheromone traps were hung in campus for monitoring the adult population development, determining the flight activities of the insect and controlling it on IPM principles. The first adult emergence of I. sexdentatus in Baglica took place in the first half of April, the highest flight activity was in April. Ips sexdentatus produced three generations in the region. The highest numbers of adults caught in traps were 741 (27 July 2021) and 421 (25 April 2022), respectively. In the Baglica Campus, a total of over 19,000 insects were caught and eliminated. Almost 328 tC of carbon stock was preserved and prevented from being released into nature and at least 11.100 black pine trees were saved or 26.640 USD was contributed to the economy. Using pheromone traps for the control of I. sexdentatus is recommended as a sustainable method that protects biodiversity, without any disturbance of the ecological balance.Item Evaluation of The Use of Plant Protection Products in Türkiye and in The World and Recommendations(KSU TARIM VE DOGA DERGISI-KSU JOURNAL OF AGRICULTURE AND NATURE, 2024-04-17) Cem-ErdoganThe agricultural sector faces a wide range of local and global risks such as increasing food demand, rapid increase in world population, gradual decrease in fertile agricultural land, loss of biodiversity, environmental pollution, climate change, drought, increasing number of harmful organisms limiting crop production, resistance to plant protection products (PPPs), negative effects of PPPs on beneficial insects, residue, young population moving away from agriculture, etc. Nowadays, chemical control is the most preferred method of controlling diseases, pests and weeds that affect yield and quality in agricultural production, and Plant Protection Products (PPPs) are used. In 2022, 55,374 tonnes of PPP was used in our Turkiye. In Turkiye, PPP usage in the rate per hectare is 2.26 kg/ha, which is quite low compared to developed countries. However, in the Mediterranean, Aegean and Marmara regions where agricultural production activities are intensively carried out, the amount of PPP consumption is high. The use of PPP by groups in the world, it has increased by 53% to 111% compared to the 1990s. The use of PPPs in agriculture in the world is 3.5 million tonnes of active ingredients in 2021 with an increase of 4% compared to 2020, and the total pesticide trade is 7.1 million tonnes of formulated products with a total value of 43.2 billion USD. In this study, the use of PPPs in the world and our country was analysed and recommendations were made.Item Emotional Wellbeing and Life Satisfaction of Singles and Mated People Across 12 Nations(EVOLUTIONARY PSYCHOLOGICAL SCIENCE, 2024-12) Apostolou, Menelaos; Tekes, Burcu; Blachnio, Agata; Sullman, Mark; Costello, WilliamThe increasing occurrence of singlehood raises the question of whether people enjoy greater emotional wellbeing alone or in an intimate relationship. Guided by an evolutionary theoretical framework of human emotions, the current research aimed to address whether individuals are emotionally better off single than in an intimate relationship, taking a cross-cultural perspective. The quality of the relationship is also crucial; thus, the study also aimed to determine whether individuals in a good or bad intimate relationship differ from each other and from those who are single in terms of emotional wellbeing. In a sample of 6338 participants from 12 nations, we found that singles experienced lower emotional wellbeing and life satisfaction than those in relationships. More specifically, participants who were in a relationship or married reported the highest life satisfaction and emotional wellbeing, while those involuntarily single reported the lowest levels, with individuals who are between relationships or voluntarily single reporting intermediate levels. Additionally, participants in a good relationship experienced higher emotional wellbeing and life satisfaction than those in a bad relationship. The findings among the involuntarily single participants were similarly negative, but to a lesser extent than those in a bad relationship. These results were consistent across the different nations in our sample.Item Risk Assessment and Selection of Plant Protection Products to be Used in Integrated Pest Management Programmes(JOURNAL OF TEKIRDAG AGRICULTURE FACULTY-TEKIRDAG ZIRAAT FAKULTESI DERGISI, 2024-05-01) Erdogan, CemIn Turkiye, it is important to carry out agricultural production in a sustainable manner by protecting biodiversity. Our country's agricultural sector has various problems in production, some of which have become chronic. There are many problems affecting agricultural production and productivity such as decreasing arable agricultural areas, increasing food demand, young generation moving away from agriculture, input costs, rural development, prevalence of small family farming and consequently fragmented land structure and climate change. One of the reasons affecting productivity in production is diseases, pests and weeds in agricultural production. The way of sustainable agricultural production by protecting biological diversity is through the implementation of Integrated Pest Management (IPM). In Integrated Pest Management, it is essential to use all control methods against agricultural pests in harmony, and biological, biotechnical and cultural measures are prioritised. As a last resort, the application of Plant Protection Products (PPPs) is desired. For this reason, the PPS to be used should not be harmful to human health, should not cause environmental pollution, should not adversely affect parasitoids, predators, pollinators and should not cause residues in the products. In other words, it is essential that the application of PPPs should not be carried out randomly and unconsciously, but in a sustainable manner based on reason, science, knowledge and in a way that will help the conservation of biological diversity. In the selection of PPPs to be used in Integrated Pest Management, risk assessments are made by considering the effects of active substances on mammals, fish, non-target organisms (parasitoids, predators) and honey bees and their persistence in soil in order to reveal the risks that may occur in terms of human and environmental health, and priority is given to PPPs such as biologics and insect growth regulators. As a result of the risk assessment studies carried out, a total of 734 PPPs, including 495 active substances, 204 mixtures, 13 biological preparations, 21 biological control agents and 1 safener, were examined and the appropriate ones were presented to the service of our producers and our country's agriculture in the integrated control technical instructions.Item Comprehensive Analysis Of The Crispr-Cas Systems In Streptococcus Thermophilus Strains Isolated From Traditional Yogurts(ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, 2024-12) Ozcan, Ali; Yibar, Artun; Kiraz, Deniz; Ilikkan, Ozge KahramanPhage resistance is crucial for lactic acid bacteria in the dairy industry. However, identifying all phages affecting these bacteria is challenging. CRISPR-Cas systems offer a resistance mechanism developed by bacteria and archaea against phages and plasmids. In this study, 11 S. thermophilus strains from traditional yogurts underwent analysis using next-generation sequencing (NGS) and bioinformatics tools. Initial characterization involved molecular ribotyping. Bioinformatics analysis of the NGS raw data revealed that all 11 strains possessed at least one CRISPR type. A total of 21 CRISPR loci were identified, belonging to CRISPR types II-A, II-C, and III-A, including 13 Type II-A, 1 Type III-C, and 7 Type III-A CRISPR types. By analyzing spacer sequences in S. thermophilus bacterial genomes and matching them with phage/plasmid genomes, notable strains emerged. SY9 showed prominence with 132 phage matches and 30 plasmid matches, followed by SY12 with 35 phage matches and 25 plasmid matches, and SY18 with 49 phage matches and 13 plasmid matches. These findings indicate the potential of S. thermophilus strains in phage/plasmid resistance for selecting starter cultures, ultimately improving the quality and quantity of dairy products. Nevertheless, further research is required to validate these results and explore the practical applications of this approach.Item Comparative Genomics Of Four Lactic Acid Bacteria Identified With Vitek Ms (Maldi-Tof) And Whole-Genome Sequencing(MOLECULAR GENETICS AND GENOMICS, 2024-11) Kahraman-Ilikkan, OzgeLactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and identification are essential. Recent advances in omics technologies and high-throughput sequencing have made the identification and characterization of bacteria. This study firstly aimed to demonstrate the sensitivity of the Vitek MS (MALDI-TOF) system in the identification of lactic acid bacteria and, secondly, to characterize bacteria using various bioinformatics approaches. Probiotic potency-related genes and secondary metabolite biosynthesis gene clusters were examined. The Vitek MS (MALDI-TOF) system was able to identify all of the bacteria at the genus level. According to whole genome sequencing, the bacteria were confirmed to be Lentilactobacillus buchneri, Levilactobacillus brevis, Lactiplantibacillus plantarum, Levilactobacillus namurensis. Bacteria had most of the probiotic potency-related genes, and different toxin-antitoxin systems such as PemIK/MazEF, Hig A/B, YdcE/YdcD, YefM/YoeB. Also, some of the secondary metabolite biosynthesis gene clusters, some toxic metabolite-related genes, and antibiotic resistance-related genes were detected. In addition, Lentilactobacillus buchneri Egmn17 had a type II-A CRISPR/Cas system. Lactiplantibacillus plantarum Gmze16 had a bacteriocin, plantaricin E/F.Item Copy Number Variations Of Stepwise-Selected Doxorubicin-Resistant Mcf-7 Cell Lines(GENE, 2025-02) Acinan, Irem Sinem; Kazan, Hasan Huseyin; Kandemir, Basak; Karahan, Ceyhan Piril; Kayhan, Guelsuem); Iseri, Ozlem DarcansoyElimination of cytotoxic effect in cells with multidrug resistance (MDR) phenotype is a situation that is gradually acquired over time and develops through multiple pathways resulting in global phenotypic changes of cells. Although molecular background of the resistance phenotype has widely been studied in the gene expression level, segmental and gene copy number variations (CNVs) have limitedly been documented. Thus, in the present study, we aimed to analyze the CNVs using DNA microarray in the sensitive and two doxorubicin-resistant MCF-7 breast cancer cell lines which had different resistance indices. In the present study, we performed conventional karyotyping and array comparative genomic hybridization (aCGH). Then, results of aCGH data were studied with genomic profiling, comparison analysis and ideogram plotting to evaluate genomic profiles, and the loss and gains of heterozygosity profiles. Next, gene lists for each cell line were compared with the 66-breast cancer- related genes and the multidrug resistance-related genes. aCGH analyses showed that CNV profiles and the copy number of specific genes were dramatically different between these three cell lines. Totally, 6212, 6558, and 11,201 genes were found to be altered in MCF-7, MCF-7/400DOX, and MCF-7/1000DOX genomes, respectively. Amongst the MCF-7/1000DOX had the highest number of altered genes, and doxorubicin resistance may cause differential chromosomal changes depending on the resistance status. DNA microarray would be one of the informative methods used in the studies on the cancer drug resistance in addition to transcriptomic and proteomic level high throughput analysis to define molecular mechanisms of the resistance status.