WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 2Citation - Scopus: 2Effect of Mirna Administration on Non-Small Cell Lung Cancer Cells Studied by Cellular Viability Assay and Atr-Ftir Spectroscopy Combined With Multivariate Data-Analysis(Elsevier, 2025) Dagdeviren, Melih; Guler, Gunnur; Guler, Egemen Erdem; Un, Cemal; Karabay-Yavasoglu, Nefise UlkuMicroRNAs (miRNAs), small non-coding RNAs, play a significant role in the regulation of gene expression by various mechanisms. Some miRNAs such as hsa-miR-145 (mir145), hsa-let-7a-1 (let7), hsa-miR-155 (mir155), and hsa-miR-29b (mir29b) are expressed at low levels in cancers and associated with proliferation, metastasis, invasion and apoptosis. In the current study, we aimed to investigate the effect of selected synthetic miRNAs and their combinations on the non-small cell lung cancer (NSCLC) cells (A549) by following the cell viability profile and alterations in the cellular biomolecules with biophysical features. After administration of commercial miRNAs and their various combinations to A549 cell line, each group was analyzed with cell viability assay and attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy combined with unsupervised multivariate analysis. Bioinformatics analysis was also performed to detect and to classify the target human genes obtained from the mirDB database. According to the cell viability results, the "mir29b + let7" combination and "mir155" significantly decreased the cancer cell viability whereas the "mir145 + mir29b" and "mir155 + mir145" combinations dramatically increased the cancer cell viability when compared to the control cells. The FTIR data revealed that administration of the "mir155", "mir29b + let7 + mir155", and "mir29b + let7" combinations caused a decrease in the contents of proteins, lipids and nucleic acids in A549 cells. This study suggests that those miRNA combinations might be potential targets for vaccines or miRNA-based therapies that can restore the miRNA activity and thus should be further evaluated to combat lung cancer with miRNA technology.Review Citation - WoS: 5Scientists Without Borders: Lessons From Ukraine [2](Oxford Univ Press, 2023) Wolfsberger, Walter; Chhugani, Karishma; Shchubelka, Khrystyna; Frolova, Alina; Salyha, Yuriy; Zlenko, Oksana; Arych, MykhailoConflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades' worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.Article Citation - WoS: 44Hesperidin Promotes Programmed Cell Death by Downregulation of Nongenomic Estrogen Receptor Signalling Pathway in Endometrial Cancer Cells(Elsevier Ltd., 2018) Cincin, Zeynep Birsu; Kıran, Bayram; Baran, Yusuf; Çakmakoğlu, BediaEndometrial carcinoma (EC) is the most common malignant gynecologic tumor in women. EC is thought to be caused by increasing estrogen levels relative to progesterone in the body. Hesperidin (Hsd), a biologically active flavonoid, could be extracted from Citrus species. It has been recently shown that Hsd could exert anticarcinogenic properties in different cancer types. However, the effects of Hsd and its molecular mechanisms on EC remain unclear. In this study, the antiproliferative, apoptotic and genomic effects of Hsd in EC and its underlying mechanisms were identified. We found that Hsd significantly suppressed the proliferation of EC cells in dose and time dependent manner. Mechanistic studies showed that Hsd could contribute apoptosis by inducing externalization of phosphatidyl serine (PS), caspase-3 activity and loss of mitochondrial membrane (MMP). Furthermore, we examined that Hsd could also significantly upregulate the expression of proapoptotic Bax subgroup genes (Bax and Bik) while downregulating the anti-apoptotic protein Bcl-2 in EC cell lines. According to GO enrichment and KEGG pathway analysis of differentially expressed genes in Hsd treated EC cells, we identified that Hsd could promote cell death via downregulation of estrogen receptor I (ESRI) that was directly related to ERK/MAPK pathway. Taken together, our study first showed that Hsd could be an antiestrogenic compound that could modulate nongenomic estrogen receptor signaling through inhibition of EC cell growth. Our findings may provide us a novel growth inhibitory agent for EC treatment after verifying its molecular mechanism with in vivo studies.Article Citation - WoS: 2Citation - Scopus: 5Pgminer: Complete Proteogenomics Workflow; From Data Acquisition To Result Visualization(Elsevier Ltd., 2017) Has, Canan; Allmer, JensIn parallel with the development of nucleotide sequencing an equally important interest in further describing the sequence in terms of function arose and the latter represents the current bottleneck in the overall research question. Sequencing the transcriptome allows determination of expressed nucleotide sequences and using mass spectrometry allows sequencing on the protein level. Both approaches can only sequence a subset of the existing transcripts. Moreover, for example post translational modification events can only be determined on the proteomics level. Therefore, it is essential to combine proteomics and genomics. For that purpose, proteogenomics data analysis pipelines have been described. Here, we describe a novel proteogenomics workflow which encompasses everything from the acquisition of data to result visualization in the Konstanz Information Miner (KNIME), a state of the art workflow management and data analytics platform. We amended KNIME with a number of processes like peptide consensus prediction, peptide mapping, and database equalizing, as well as result visualization. This enabled construction of our new workflow, entitled PGMiner, which not only includes all data analysis steps, but is highly customizable which is rather cumbersome for most existing pipelines. Furthermore, no burdensome installation processes have to be performed making PGMiner the most user friendly tool available.