Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
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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 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.Letter Citation - Scopus: 9A Call for Benchmark Data in Mass Spectrometry-Based Proteomics(Proteomass Scientific Society, 2012) Allmer, JensProteomics is a quickly developing field. New and better mass spectrometers, the platform of choice in proteomics, are being introduced frequently. New algorithms for the analysis of mass spectrometric data and assignment of amino acid sequence to tandem mass spectra are also presented on a frequent basis. Unfortunately, the best application area for these algorithms cannot be established at the moment. Furthermore, even the accuracy of the algorithms and their relative performance cannot be established. This is due to the lack of proper benchmark data. This letter first introduces the field of mass spectrometry-based proteomics and then defines the expectations of a well-designed benchmark dataset. Thereafter, the current situation is compared to this ideal. A call for the creation of a proper benchmark dataset is then placed and it is explained how measurement should be performed. Finally, the benefits for the research community are highlighted. © 2012, Proteomass Scientific Society. All rights reserved.Article Citation - WoS: 2Citation - Scopus: 2Identification of Cytoplasmic Sialidase Neu2-Associated Proteins by Lc-ms/Ms(Türk Biyokimya Derneği, 2019) Akyıldız Demir, Seçil; Seyrantepe, VolkanBackground: Cytoplasmic sialidase (NEU2) plays an active role in removing sialic acids from oligosaccharides, gly-copeptides, and gangliosides in mammalian cells. NEU2 is involved in various cellular events, including cancer metabolism, neuronal and myoblast differentiation, proliferation, and hypertrophy. However, NEU2-interacting protein(s) within the cell have not been identified yet. Objective: The aim of this study is to investigate NEU2 interacting proteins using two-step affinity purification (TAP) strategy combined with mass spectrometry analysis. Methods: In this study, NEU2 gene was cloned into the pCTAP expression vector and transiently transfected to COS-7 cells by using PEI. The most efficient expression time of NEU2- tag protein was determined by real-time PCR and Western blot analysis. NEU2-interacting protein(s) were investigated by using TAP strategy combined with two different mass spectrometry experiment; LC-MS/MS and MALDI TOF/TOF. Results: Here, mass spectrometry analysis showed four proteins; a-actin, beta-actin, calmodulin and histone H1.2 proteins are associated with NEU2. The interactions between NEU2 and actin filaments were verified by Western blot analysis and immunofluorescence analysis. Conclusions: Our study suggests that association of NEU2 with actin filaments and other protein(s) could be important for understanding the biological role of NEU2 in mammalian cells.Editorial Citation - WoS: 3Citation - Scopus: 4La médecine de précision en oncologie: challenges, enjeux et nouveaux paradigmes(John Libbey Eurotext Ltd, 2019) Cox, Stephanie; Rousseau-Tsangaris, Marina; Abou-Zeid, Nancy; Dalle, Stephane; Leurent, Pierre; Cutivet, Arnaud; Baran, YusufL'oncologie médicale a pris, depuis quelques années, un tournant substantiel en intégrant la dimension génomique dans la prise de décision thérapeutique. En raison de l'accès aux technologies de séquençage (exome complet, séquençage ciblé du génome, séquençage de l'ARN, ADN circulant. . .) facilité par la mise en place de plateformes de biologie moléculaire et la diminution des coûts par échantillon, la caractérisation moléculaire est devenue un outil supplémentaire à la disposition du clinicien, s'ajoutant au diagnostic histologique et immunohistochimique et aux données d'imagerie radiologique. Cette approche moléculaire a permis d'identifier de nouvelles formes nosologiques et permet, au-delà de l'aspect cognitif, de renseigner sur les altérations qui sont à prendre en compte dans les décisions thérapeutiques (biomarqueurs prédictifs, activation de voies spécifiques, mutations de résistance). C'est dans ce contexte de profond et rapide changement de pratique médicale et scientifique qu'il a été proposé de réfléchir collectivement aux nouveaux enjeux sous la forme d'un workshop à l'occasion de Biovision qui s'est tenu à Lyon, du 4 au 6 avril 2017.Article Citation - WoS: 3Citation - Scopus: 3Frequency and Levels of Potential Drug-Drug Interactions in Tuberculosis Patients of a Teaching Hospital in Pakistan(Colegio de Farmaceuticos de la Provincia de Buenos Aires, 2016) Uddin, Fayyaz; Khan, Nasar; Ghani, Shamsul; Khan, Saeed A.Polypharmacy in tuberculosis is used to prevent occurrence of resistance to mycobacteria. However, drug-drug interaction is one of the undesirable consequences of polypharmacy, that may lead to ineffective medication or change in therapeutic response. The objective of the study was to identify prevalence, types and nature of potential drug-drug interactions in tuberculosis patients at Khyber Teaching Hospital, Peshawar Pakistan. Medical records of 409 randomly-selected patients were reviewed for pDDIs using Micromedex Database. Results show that total 304 interacting-combinations lead to 1437 potential drug-drug interactions. 87.5% of the these potential drug-drug interactions were of moderate and major severity (i.e., 65.6% and 44.3% respectively). With regards to scientific-evidence, almost 50% of the potential drug-drug interactions were good documented while 34.7% had fair level of documentation. Furthermore, we have listed some of the interacting drug combinations, particularly most frequent major and moderate interactions, will help health care professionals to review their established therapeutic strategy for tuberculosis patients in their clinical settings.Article Citation - WoS: 3Citation - Scopus: 3A Minimally Invasive Transfer Method of Mesenchymal Stem Cells To the Intact Periodontal Ligament of Rat Teeth: a Preliminary Study(TÜBİTAK, 2018) Gül Amuk, Nisa; Kurt, Gökmen; Kartal Yandım, Melis; Adan, Aysun; Baran, YusufThe aim of this study was to introduce a minimally invasive procedure for mesenchymal stem cell (MSC) transfer into the intact periodontal ligament (PDL) of the molar teeth in rats. Ten 12-week-old Wistar albino rats were used for this preliminary study. MSCs were obtained from bones of two animals and were labeled with green fluorescent protein (GFP). Four animals were randomly selected for MSC injection, while 4 animals served as a control group. Samples were prepared for histological analysis, Cox-2 mRNA expression polymerase chain reaction analysis, and fluorescent microscopy evaluation. The number of total cells, number of osteoclastic cells, and Cox-2 mRNA expression levels of the periodontal tissue of teeth were calculated. The number of total cells was increased with MSC injections in PDL significantly (P < 0.001). The number of osteoclastic cells and Cox-2 mRNA expression were found to be similar for the two groups. GFP-labeled MSCs were observed with an expected luminescence on the smear samples of the PDL with transferred MSCs. The results of this preliminary study demonstrate successful evidence of transferring MSCs to intact FIX in a nonsurgical way and offer a minimally invasive procedure for transfer of MSCs to periodontal tissues.Article Citation - WoS: 9Citation - Scopus: 10Effects of Notch Signalling on the Expression of Sema3c, Hmga2, Cxcl14, Cxcr7, and Ccl20 in Breast Cancer(TÜBİTAK, 2019) Küçükköse, Cansu; Yalçın Özuysal, ÖzdenMetastasis is the main reason for death in breast cancer. Understanding the molecular players in metastasis is crucial for diagnostic and therapeutic purposes. Notch signalling plays an oncogenic role in breast tumorigenesis and is involved in metastasis. Downstream mediators of Notch signalling in prometastatic processes are not yet fully discovered. Here we aimed to investigate whether Notch signalling regulates the expression of SEMA3C, HMGA2, CXCL14, CXCR7, and CCL20, which are involved in prometastatic processes, in breast cell lines. To this end, expression of the selected genes was analysed following Notch activation by overexpression of the Notch1 intracellular domain in the normal breast epithelial cell line MCF10A, and inhibition by silencing of the Notch transcriptional mediator RBPj kappa in the breast cancer cell line MDA MB 231. SEMA3C and HMGA2 mRNA were decreased, while CXCL14 and CXCR7 mRNA were increased significantly in response to Notch activation in MCF10A cells. Notch inhibition in MDA MB 231 cells significantly decreased HMGA2 and CCL20 mRNA. Protein levels were not significantly altered by Notch modulation. In conclusion, we showed that Notch signalling regulates expression of SEMA3C, CXCL14, CCL20, CXCR7, and HMGA2, which are prominent candidate genes that might function downstream of Notch to induce prometastatic processes.Article Citation - WoS: 24Citation - Scopus: 29Il-17, Il-21, and Il-22 Cytokines of T Helper 17 Cells in Cancer(Mary Ann Liebert, 2019) Nalbant, AytenCD4(+) T helper (Th) cells are important regulators of cellular immune response. Newly discovered interleukin (IL)-17-producing CD4(+) T cells are known as T helper 17 cells (Th17). They are distinct subset from the T helper type 1 (Th1) and 2 (Th2) lineages. The differentiation of Th17 cells has been intensively studied; however, the role of Th17 cells in different diseases including cancer is still under investigation. Besides IL-17 family cytokines, Th17 cells produce IL-22, IL-21, and IL-26. The dysregulated function of Th17 cells and their cytokines could contribute to pathology of diseases, including cancer. The role of cytokines of Th17 cells such as IL-17, IL-21, and IL-22 in cancer will be discussed in this review.