Fen Edebiyat Fakültesi / Faculty of Letters and Science

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    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.
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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.
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    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.
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    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.
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    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.
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    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.