Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Data Paper Knockdown of Death Receptor 5 Antisense Long Noncoding Rna and Cisplatin Treatment Modulate Similar Macromolecular and Metabolic Changes in Hela Cells(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2022) Gürer, Dilek Cansu; Erdoğan Vatansever, İpek; Ceylan, Çağatay; Akgül, BünyaminBackground/aim: Despite great progress in complex gene regulatory mechanisms in the dynamic tumor microenvironment, the potential contribution of long noncoding RNAs (lncRNAs) to cancer cell metabolism is poorly understood. Death receptor 5 antisense (DR5-AS) is a cisplatin inducible lncRNA whose knockdown modulates cell morphology. However, its effect on cell metabolism is unknown. The aim of this study is to examine metabolic changes modulated by cisplatin and DR5-AS lncRNA in HeLa cells. Materials and methods: We used cisplatin as a universal cancer therapeutic drug to modulate metabolic changes in HeLa cervix cancer cells. We then examined the extent of metabolic changes by Fourier transform infrared spectroscopy (FTIR). We also performed transcriptomics analyses by generating new RNA-seq data with total RNAs isolated from cisplatin-treated HeLa cells. Then, we compared cisplatin-mediated transcriptomics and macromolecular changes with those mediated by DR5-AS knockdown. Results: Cisplatin treatment caused changes in the unsaturated fatty acid and lipid-to-protein ratios and the glycogen content. These observations in altered cellular metabolism were supported by transcriptomics analyses. FTIR spectroscopy analyses have revealed that DR5-AS knockdown causes a 20.9% elevation in the lipid/protein ratio and a 76.6% decrease in lipid peroxidation. Furthermore, we detected a 3.42% increase in the chain length of the aliphatic lipids, a higher content of RNA, and a lower amount of glycogen indicating relatively lower metabolic activity in the DR5-AS knockdown HeLa cells. Interestingly, we observed a similar gene expression pattern under cisplatin treatment and DR5-AS knockdown HeLa cells. Conclusion: These results suggest that DR5-AS lncRNA appears to account for a fraction of cisplatin-mediated macromolecular ametabolic changes in HeLa cervix cancer cells.Article Citation - WoS: 1Citation - Scopus: 1Cytoplasmically Localized Trna-Derived Fragments Inhibit Translation in Drosophila S2 Cells(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2022) Hamid, Syed Muhammad; Akgül, BünyaminTransfer ribonucleic acids (tRNAs) serve not only as amino acid carriers during translation but also as a template for the biogenesis of short fragments that can regulate gene expression. Despite recent progress in the function of tRNA-derived fragments (tRFs), their intracellular localization, protein partners, and role in regulating translation are not well understood. We used synthetic tRFs to investigate their localization and function in Drosophila S2 cells. Under our experimental setting, all synthetic tRFs tested were localized at distinct sites within the cytoplasm in a similar manner in Drosophila S2 cells. Cytoplasmically-localized tRFs were positioned in close proximity to GW182 and XRN1 proteins. Functionally, tRFs, which slightly suppressed proliferation in S2 cells, inhibited translation without any major shift in the polysome profile. These results suggest that 5???-tRFs are cytoplasmically-localized and regulate gene expression through inhibition of translation in Drosophila.Article Citation - WoS: 3Citation - Scopus: 3Evaluation of Variation on Myostatin (mstn) Gene of Turkish Donkey Populations in Thrace Region of Turkey(Namık Kemal Üniversitesi, 2022) Işık, Raziye; Özdil, Fulya; Meral, SenaThe study aimed to determine the MSTN gene variation in 90 donkeys reared in the Thrace region of Turkey. Myostatin (MSTN), also named GDF-8 (growth differentiation factor 8) is a part of the transforming growth factor beta (TGF-beta) superfamily and it has a negative regulator role on muscle mass, growth and development in mammalian species. MSTN gene regulates the skeletal muscle growth in a negative way and has a significant role in homeostasis of skeletal muscles. Also, in muscle fibers balance of protein has been promoted by Myostatin factor. The total of 866 bp long partial intron 1 and 2, whole exon 2 regions of MSTN gene was amplified and PCR products analysed using DNA sequencing. In this study, a novel synonymous SNP was determined as g.4183919 G>A in the second exon region of the MSTN gene which does not cause an amino acid change in the protein. The G>A transition caused a silent mutation in leucine (leu) amino acid. Alterations in mRNA level and functionality of protein can occur due to synonymous mutations. Since leucine is an important amino acid that can avoid muscle mass loss and inhibits the expression of Myostatin, it can be said that silent mutation of Leu in donkeys may have altered the muscle mass and physical factor of donkeys in this study. Mutant leucine may have a lower efficient effect on preventing loss of muscles and causes more Myostatin protein expression. The identified SNP was firstly released and the DNA sequences of the MSTN gene in Turkish donkeys was revealed for the first time with recent study. Turkish donkeys lacked these mutations that were identified before in horses, which cause for the less might require for race ability of donkeys. The sequences of MSTN gene were submitted to the NCBI GenBank with the accession number: MW970078- MW970079. Further studies are needed to conduct, on protein and molecular levels, SNPs on the MSTN gene and their association with the morphological characters that may affect economic traits in donkey breeds.Article Citation - WoS: 14Citation - Scopus: 15Noncoding Rnas in Apoptosis: Identification and Function(TÜBİTAK, 2022) Tüncel, Özge; Kara, Merve; Yaylak, Bilge; Erdoğan, İpek; Akgül, BünyaminApoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, protein coding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis. However, recent genome annotations and transcriptomics studies have uncovered a plethora of regulatory noncoding RNAs that have the ability to modulate not only apoptosis but also many other biochemical processes in eukaryotes. In this review article, we will cover a brief summary of apoptosis and detection methods followed by an extensive discussion on microRNAs, circular RNAs, and long noncoding RNAs in apoptosis.Article Citation - WoS: 3Citation - Scopus: 6Improved Cell Segmentation Using Deep Learning in Label-Free Optical Microscopy Images(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2021) Ayanzadeh, Aydın; Yalçın Özuysal, Özden; Pesen Okvur, Devrim; Önal, Sevgi; Töreyin, Behçet Uğur; Ünay, DevrimThe recently popular deep neural networks (DNNs) have a significant effect on the improvement of segmentation accuracy from various perspectives, including robustness and completeness in comparison to conventional methods. We determined that the naive U-Net has some lacks in specific perspectives and there is high potential for further enhancements on the model. Therefore, we employed some modifications in different folds of the U-Net to overcome this problem. Based on the probable opportunity for improvement, we develop a novel architecture by using an alternative feature extractor in the encoder of U-Net and replacing the plain blocks with residual blocks in the decoder. This alteration makes the model superconvergent yielding improved performance results on two challenging optical microscopy image series: a phase-contrast dataset of our own (MDA-MB-231) and a brightfield dataset from a well-known challenge (DSB2018). We utilized the U-Net with pretrained ResNet-18 as the encoder for the segmentation task. Hence, following the modifications, we redesign a novel skip-connection to reduce the semantic gap between the encoder and the decoder. The proposed skip-connection increases the accuracy of the model on both datasets. The proposed segmentation approach results in Jaccard Index values of 85.0% and 89.2% on the DSB2018 and MDA-MB-231 datasets, respectively. The results reveal that our method achieves competitive results compared to the state-of-the-art approaches and surpasses the performance of baseline approaches.Article Citation - WoS: 3Citation - Scopus: 3Endogenous Heat Shock Protein Groel of A. Actinomycetemcomitans Preferentially Targets Primary Human Cd8+t Cells(TÜBİTAK, 2015) Kant, Melis; Akgül, Bünyamin; Nalbant Aldanmaz, AytenApoptosis can be used to manipulate host cells by bacterial products such as bacterial heat shock proteins (Hsp). One of the virulence factors of periodontal pathogen Aggregatibacter actinomycetemcomitans is heat shock protein GroEL (AaGroEL), which has been shown to interact with host cells. AaGroEL (Hsp64) also has the potential to modulate immune system cells. In this study we used endogenous AaGroEL protein as an antigen to study bacterial Hsp-induced apoptosis in different immune system cells. Human peripheral blood mononuclear cells and cell lines were cultured with different doses (50-1000 ng/mL) of endogenous AaGroEL at various time points. Apoptosis of the cells was measured by Annexin V and 7AAD labeling. Apoptotic cells were analyzed by flow cytometry. Our data suggested that AaGroEL-responding primary CD8+ T cells were more susceptible to apoptosis than CD4+ T cells. Furthermore, the magnitude of apoptosis in the Jurkat T cell line was higher than that in primary CD8+ T cells. There was no statistically significant level of apoptosis in the chronic myeloid leukemia (K562) cell line, which belongs to myeloid lineages. Thus, A. actinomycetemcomitans GroEL protein has more potent apoptotic effect on cells that are derived from a lymphoid progenitor.Article Characterization of the Human Sialidase Neu4 Gene Promoter(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2014) Seyrantepe, Volkan; Delman, MuratThere are 4 different sialidases that have been described in humans: lysosomal (Neu1), cytoplasmic (Neu2), plasma membrane (Neu3), and lysosomal/mitochondrial (Neu4). Previously, we have shown that Neu4 has a broad substrate specificity and is active against glyco-conjugates, including GM2 ganglioside, at the acidic pH of 3.2. An overexpression of Neu4 in transfected neuroglia cells from a Tay-Sachs patient shows a clearance of accumulated GM2, indicating the biological importance of Neu4. In this paper, we aimed to characterize a minimal promoter region of the human Neu4 gene in order to understand the molecular mechanism regulating its expression. We cloned 7 different DNA fragments from the human Neu4 promoter region into luciferase expression vectors for a reporter assay and also performed an electrophoretic mobility shift assay to demonstrate the binding of transcription factors. We demonstrated that -187 bp upstream of the Neu4 gene is a minimal promoter region for controlling transcription from the human Neu4 gene. The electrophoretic mobility shift assay showed that the minimal promoter region recruits a c-myc transcription factor, which might be responsible for regulation of Neu4 gene transcription. The data we obtained might be useful to discover small molecules, which control selective high expression of the human Neu4 gene, resulting in the normal morphological phenotype in the lysosomes of Tay-Sachs patients.Article Thrips parazitoiti Ceranisus (Hymenoptera: Eulophidae) cinsinin morfolojik yapı ve 28S D2 rDNA temelinde Türkiye’deki güncel taksonomik durumları(Türkiye Entomoloji Derneği, 2010) Doğanlar, Oğuzhan; Doğanlar, Mikdat; Frary, AnneÇalışma ile Mayıs 2006 ile Mayıs 2007 tarihleri arasında Güneydoğu Anadolu Bölgesi ve Akdeniz Bölgesi’nin doğusunda bulunan Ceranisus (Hymenoptera: Eulophidae) cinsi ve benzer diğer cinslerin genetik analizleri yapılarak, bu verilerin diğer thrips parazitoitlerinin morfolojik yapılarıyla mukayese edilip, türlerin kesin teşhislerinin yapılması amaçlanmıştır. Bu kapsamda, Hatay, Gaziantep, Adıyaman ve Şanlıurfa’da 38 farklı noktada örnekleme yapılmış ve 20 örnekleme noktasında toplam 143 adet (30 erkek; 113 dişi) Ceranisus cinsine giren tür toplanmıştır. Populasyon morfolojik özelliklerine göre 13 farklı gruba ayrılmıştır. Bu türlerin filogenetik ilişkileri DNA dizileri kullanılarak verilmiştir. Toplam 15 tür 28S D2 ribosomal DNA bölgesi kullanılarak analiz edilmiştir. Analiz sonucunda morfolojik olarak ayrılan 13 farklı tür grubundan 3 tanesinin genetik olarak farklı olduğu görülmüştür. Diğer türlerden ise 4 adetinin C. nr. lepidotus grubu oluşturdukları, 5 adet C. nr. bozovaensis’in ise kendi aralarında 2 farklı grup oluşturdukları belirlenmiştir. Sonuç olarak 3 adet yeni Ceranisus türü, bunun haricinde 3 adet farklı türü oluşturabilecek popülasyon genetik olarak belirlenmiştir.Article Sitokinlerin Hücre Döngüsü Üzerinde Etkileri(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 1999) Güneş, HaticeSitokinler hücresel düzenleyici proteinlerdir. Vücudun farklı dokularında çesitli hücreler tarafından belli uyarıcılara karsı salgılanıp pek çok farklı biyolojik fonksiyonları kontrol eden sitokinlerin en önemli etkilerinden biri hücre bölünmesi üzerindedir. Bazı sitokinler hücre döngüsünün ilerlemesinde pozitif rol oynarken, bazıları hücre bölünmesini engelleyici etki gösterirler. Sitokinlerin hücre bölünmesi üzerindeki pozitif ve negatif etkileri hücre tipine baglı olarak degisir. Burada bazı sitokinlerin hücre döngüsü üzerindeki etkilerinin moleküler mekanizmaları anlatılmıstır.Article Citation - WoS: 6Citation - Scopus: 6Therapeutic Potentials of Inhibition of Jumonji C Domain-Containing Demethylases in Acute Myeloid Leukemia(Aves, 2020) Koca, Duygu; Hastar, Nurcan; Engür, Selin; Kiraz, Yağmur; Ulu, Gizem Tuğçe; Çekdemir, Demet; Baran, YusufAcute myeloid leukemia (AML) is a complex disease affected by both genetic and epigenetic factors. Histone methylation and demethylation are types of epigenetic modification in chromatin remodeling and gene expression. Abnormal expression of histone demethylases is indicated in many types of cancer including AML. Although many commercial drugs are available to treat AML, an absolute cure has not been discovered yet. However, inhibition of demethylases could be a potential cure for AML. Methylstat is a chemical agent that inhibits the Jumonji C domain-containing demethylases.
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