Fen Edebiyat Fakültesi / Faculty of Letters and Science

Permanent URI for this collectionhttps://hdl.handle.net/11727/1396

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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, Regine
Partial 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.
Advancements in QTL Mapping and GWAS Application in Plant Improvement
(TURKISH JOURNAL OF BOTANY, 2024) Altaf, Muhammad Tanveer; Tatar, Muhammed; Ali, Amjad; Liaqat, Waqas; Mortazvi, Parnaz; Kayihan, Ceyhun; Olmez, Fatih; Nadeem, Muhammad Azhar; Javed, Jazib; Gou, Jin-Ying; Wang, Meng-Lu; Umar, Ummad Ud Din; Dasgan, Hayriye Yildiz; Kurt, Cemal; Yildiz, Mehtap; Mansoor, Sheikh; Dababat, Abdelfattah A.; Celiktas, Nafiz; Baloch, Faheem Shehzad
In modern plant breeding, molecular markers have become indispensable tools, allowing the precise identification of genetic loci linked to key agronomic traits. These markers provide critical insight into the genetic architecture of crops, accelerating the selection of desirable traits for sustainable agriculture. This review focuses on the advancements in quantitative trait locus (QTL) mapping and genome-wide association studies (GWASs), highlighting their effective roles in identifying complex traits such as stress tolerance, yield, disease resistance, and nutrient efficiency. QTL mapping identifies the significant genetic regions linked to desired traits, while GWASs enhance precision using larger populations. The integration of high-throughput phenotyping has further improved the efficiency and accuracyof QTL research and GWASs, enabling precise trait analysis across diverse conditions. Additionally, next-generation sequencing, clustered regularly interspaced short palindromic repeats (CRISPR) technology, and transcriptomics have transformed these methods, offering profound insights into gene function and regulation. Single-cell RNA sequencing further enhances our understanding of plant responses at the cellular level, especially under environmental stress. Despite this progress, however, challenges persist in optimizing methods, refining training populations, and integrating these tools into breeding programs. Future studies must aim to enhance genetic prediction models, incorporate advanced molecular technologies, and refine functional markers to tackle the challenges of sustainable agriculture.
Biochemical And Molecular Analyses Of Insecticide Resistance In Greenhouse Populations Of Bemisia Tabaci (Hemiptera: Aleyrodidae) In Türkiye
(Başkent Üniversitesi Fen Edebiyat Fakültesi, 2024-04-04) Erdogan, Cem; Toprak, Umut; Gurkan, M. Oktay
The sweet potato/cotton whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is one of the most destructive vegetable pests in greenhouses in Turkiye. While the preferred method of control primarily relies on insecticides such as neonicotinoids, organophosphates and pyrethroids, their intensive use has caused whiteflies to rapidly become resistant. Samples were collected from 13 Turkish B. tabaci greenhouse populations. Bioassays from the Marmara Region identified as high as a 53-fold increase in resistance to chlorpyrifos-ethyl, a 303-fold increase to imidacloprid and a 282-fold increase to acetamiprid. Bioassays in the Central Anatolia Region reported a 76-fold increase in resistance to deltamethrin and-15-fold increase to thiamethoxam. Most of the populations showed cross-resistance for neonicotinoids. All collected B. tabaci populations were determined to be MEAM 1 (also referred to as biotype B) for diagnostic band E0.14. The E0.14 esterase variant that helps to diagnose biotype B insects was found in all individuals from field populations. Almost all populations showed higher non-specific esterase, glutathione-S-transferase (GST) and monooxygenase activity when compared to susceptible SUD-S population. AChE insensitivity assays for individual B. tabaci suggest a target-site modification as a mechanism of resistance to chlorpyrifos-ethyl. This is the first report of AChE variants identified based on their sensitivities to chlorpyrifos ethyl-oxon and pirimicarb in Turkish B. tabaci populations. Fixed ace mutations in the target-site of organophosphates and pyrethroids were identified in six populations. Resistance to organophosphates and neonicotinoids were at least partially related to both ace mutations and insensitive AChE and monooxygenase activities, respectively. The results will help develop effective resistance management programs of B. tabaci in Turkiye.
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, Ozge
Lactic 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.
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 Kahraman
Phage 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.
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 Darcansoy
Elimination 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.
Determining the Dielectric Characteristics of the Au/C20H12/n-Si (MPS) Structure Over A Wide Temperature and Voltage
(INDIAN JOURNAL OF PHYSICS, 2024) Bengi, S; Altindal, S; Zeyrek, S
The temperature and voltage effects on dielectric properties (epsilon ' and epsilon ''), electric modulus (M' and M''), and ac electrical conductivity (sigma(ac)) of the fabricated Au/C20H12/n-Si (MPS) structures have been investigated in wide temperature range of 200-400 K and voltage (+/- 3 V) using C/G-V measurements at 500 kHz. The voltage and temperature dependence profile of phase-angle (theta degrees) were also extracted from the impedance (Z ' and Z ''). All these parameters were found as a function of temperature and voltage in the forward bias region due to the relaxation mechanisms and interface traps located at C20H12/n-Si interface in the bandgap of Si. The characterizations show that main dielectric parameters such as dielectric constant (epsilon'), dielectric loss (epsilon''), tangent loss (tan delta), and ac electrical conductivity (sigma(ac)) increase with increasing temperature, epsilon'-V and M''-V plots show a peak, and its magnitude and position vary with temperature due to reordering/restructure of traps and polarization under temperature and voltage effects. The E-a value was obtained from the slope of Arrhenius, Ln(sigma(ac))-q/kT), plot as 40.8 meV.
Effective Health Communication Depends on the Interaction of Message Source and Content: Two Experiments on Adherence to COVID-19 Measures in Türkiye
(PSYCHOLOGY & HEALTH, 2024) Bayrak, Fatih; Aktar, Bengi; Aydas, Berke; Yilmaz, Onurcan; Alper, Sinan; Isler, Ozan
ObjectiveFollowing the COVID-19 outbreak, authorities recommended preventive measures to reduce infection rates. However, adherence to calls varied between individuals and across cultures. To determine the characteristics of effective health communication, we investigated three key features: message source, content, and audience.MethodsUsing a pre-test and two experiments, we tested how message content (emphasizing personal or social benefit), audience (individual differences), message source (scientists or state officials), and their interaction influence adherence to preventive measures. Using fliers advocating preventive measures, Experiment 1 investigated the effects of message content and examined the moderator role of individual differences. Experiment 2 presented the messages using news articles and manipulated sources.ResultsStudy 1 found decreasing adherence over time, with no significant impact from message content or individual differences. Study 2 found messages emphasizing 'protect yourself' and 'protect your country' to increase intentions for adherence to preventive measures. It also revealed an interaction between message source and content whereby messages emphasizing personal benefit were more effective when they came from healthcare professionals than from state officials. However, message source and content did not affect vaccination intentions or donations for vaccine research.ConclusionEffective health communication requires simultaneous consideration of message source and content.
Effects of Delayed-Onset Muscle Pain on Respiratory Muscle Function
(SPORTS HEALTH-A MULTIDISCIPLINARY APPROACH, 2024-11) Ozden, Sema; Ozalp, Ozge; Kilic, Rabia Tugba; Yosmaoglu, Hayri Baran
Background: Delayed-onset muscle soreness (DOMS) has been widely examined in the peripheral muscles; however, studies showing the potential effects of DOMS on respiratory function are limited.Hypothesis: DOMS in trunk muscles has a negative effect on respiratory function parameters, respiratory muscle strength, respiratory muscle endurance, and exercise capacity.Study design: Prospective cohort study.Level of evidence: Level 2.Methods: In 24 healthy participants with a mean age of 21 +/- 2 years, DOMS was induced for the trunk muscles with a load equal to 80% of the maximum repetitive voluntary contraction. Pulmonary function parameters, respiratory muscle strength and endurance, exercise capacity, pain, fatigue, and dyspnea perception severity were recorded before DOMS and at 24 and 48 hours after DOMS.Results: After DOMS, decreases were observed in respiratory function parameters, namely, forced vital capacity, forced expiratory volume in the first second, vital capacity, and 25% to 75% flow rate value of forced expiratory volume (25% to 75%) (P = 0.02, P = 0.02, P < 0.01, P = 0.01, respectively). Maximal inspiratory pressure and exercise capacity also decreased (P = 0.02, P < 0.01, respectively). No difference was observed between all 3 measurements of maximal expiratory pressure (MEP) and MEP% values (P-1 = P-2 = P-3 >= 0.99). The results of the respiratory muscle endurance tests did not reveal a significant difference in terms of load and time in all 3 conditions (P > 0.05).Conclusion: After DOMS, there was a 4% to 7.5% decrease in respiratory function parameters, and a 6.6% decrease in respiratory muscle strength.Clinical relevance: The occurrence of DOMS before a competition can have a detrimental impact on pulmonary performance. Hence, it is imperative to consider this factor when devising training and exercise programs. In addition, the development of treatment protocols becomes crucial if DOMS arises.
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, William
The 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.
Empathy Increases Warmth Toward Syrian and Afghans, but not Ukrainians: Experimental Evidence from Türkiye
(INTERNATIONAL JOURNAL OF INTERCULTURAL RELATIONS, 2024) Aktas, Busra Eylem; Salter, Metin Ege; Yilmaz, Ayse Nur; Eker, Selin
Previous research has documented that economic concerns might limit the positive impact of empathy in reducing prejudicial attitudes toward refugees in Turkiye. Other research has also shown that religious conservatism might buffer negativity toward refugees. However, there has been no prior research testing whether empathizing with economic hardships would increase positivity toward refugees. In this study, we aimed to investigate the role of empathy by leading individuals to adopt the perspective of those experiencing the detrimental effects of resource scarcity among Turkish citizens. Specifically, we examined whether inducing empathy related to resource scarcity would increase the level of warmth felt toward Syrian, Afghan, and Ukrainian refugees, while considering the moderating roles of religiosity and conservatism in this relationship. The present study employed a between-subjects design experiment wherein participants were randomly assigned to either the control group (n = 131) or the experimental group (n = 110). The results showed that participants in the experimental group reported higher levels of warmth toward Syrians and Afghans but not toward Ukrainians when compared to the control group. Moreover, there were significant moderator roles for religiosity and conservatism in the link between induced empathy and warmth toward Syrians. Specifically, the present findings demonstrate that higher levels of religiosity and conservatism positively predict the association between empathy induction and higher levels of warmth toward Syrians but not toward Ukrainians and Afghans. Overall, these results suggest that empathizing with the scarcity of resources might be an effective approach to reducing negative attitudes toward Afghan and Syrian refugees, but it may not have the same impact on Ukrainians in the Turkish cultural context. Furthermore, these findings indicate that higher levels of conservatism and religiosity can contribute to a positive impact of empathy toward Syrians.