Moleküler Biyoloji ve Genetik Bölümü / Department of Molecular Biology and Genetics
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- PublicationOpen AccessThe Protective Effects of Sodium Pentaborate Tetrahydrate Against UVB-induced Apoptosis in Human Keratinocytes(Hitit Üniversitesi, 2022) ABDİK, EZGİ AVŞARUltraviolet radiation (UV) is an environmental carcinogen causing human skin cancer. Exposure of the skin to UV produces apoptotic keratinocytes called sunburn cells within the epidermis. Boron, an essential element for plants, has several biological properties, such as anti-cancer, anti-microbial, and anti-oxidant. In the present study, the possible protective effects of sodium pentaborate tetrahydrate (SPT) against UVB-induced apoptosis in human keratinocyte cells, HaCaT, were investigated. They were treated with SPT at different concentrations (7.8-125 μg/mL) for 24h after UVB irradiation (20, 30 and 60mJ/cm2). Cell viability, annexin V assay, cell cycle analysis, and apoptosis-related gene levels were measured using RT-PCR. Treatment with SPT (15.6-31.25μg/mL) after 30 mJ/m2 UVB exposure significantly increased cell survival. Annexin V apoptosis analysis demonstrated a robust protective effect by treatment with SPT at concentrations of 15.6 and 31.25μg/mL after 30mJ/cm2 UVB irradiation. The cell cycle analysis revealed that UVB irradiation elevated the number of cells at the G0/G1 phase while SPT treatment after UVB irradiation increased the number of cells at G2/M phase, suggesting the changes were partially reversed. Furthermore, treatment with 15.6μg/mL SPT after 30 mJ/m2 UV irradiation blocked the activation of Caspase 3, Caspase 9, Bax, And P53. These results indicate that treatment with SPT exerts protective effects after UVB irradiation. Thus, treatment with SPT led to strong protection against UVB-induced apoptotic cell death in HaCaT cells.
- PublicationOpen AccessCRISPR/Cas9-Mediated Bag-1 Knockout Increased Mesenchymal Characteristics of MCF-7 Cells Via Akt Hyperactivation-Mediated Actin Cytoskeleton Remodeling(Public Library of Science, 2022) KILBAŞ, PELİN ÖZFİLİZ; Can, Nisan Denizce; Kızılboğa, Tuğba; Ezberci, Fikret; Doğanay, Hamdi Levent; Arışan, Elif Damla; Doğanay, Gizem DinlerBag-1 protein is a crucial target in cancer to increase the survival and proliferation of cells. The Bag-1 expression is significantly upregulated in primary and metastatic cancer patients compared to normal breast tissue. Overexpression of Bag-1 decreases the efficiency of conventional chemotherapeutic drugs, whereas Bag-1 silencing enhances the apoptotic efficiency of therapeutics, mostly in hormone-positive breast cancer subtypes. In this study, we generated stable Bag-1 knockout (KO) MCF-7 breast cancer cells to monitor stress-mediated cellular alterations in comparison to wild type (wt) and Bag-1 overexpressing (Bag-1 OE) MCF-7 cells. Validation and characterization studies of Bag-1 KO cells showed different cellular morphology with hyperactive Akt signaling, which caused stress-mediated actin reorganization, focal adhesion decrease and led to mesenchymal characteristics in MCF-7 cells. A potent Akt inhibitor, MK-2206, suppressed mesenchymal transition in Bag-1 KO cells. Similar results were obtained following the recovery of Bag-1 isoforms (Bag-1S, M, or L) in Bag-1 KO cells. The findings of this study emphasized that Bag-1 is a mediator of actin-mediated cytoskeleton organization through regulating Akt activation. © 2022 Kilbas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- PublicationRestrictedEvaluation of the Spectrum of Proteolytic Activity of Micromycetes of the Genus Aspergillus in Relation to Proteins of the Hemostasis System(Pleiades Publishing, 2022) Osmolovskiy, A.A.; ŞAŞ, B.; Aleksandrova, A.V.; Baranova, N.A.; Kreyer V.G.Abstract: The activity of extracellular proteinases in seven strains of different species of micromycetes of the genus Aspergillus in relation to proteins of the hemostasis system was studied. Comparison of the values of enzymatic indices during the growth of strains on agar media with casein and fibrin, followed by their submerged fermentation fermentation and analysis of amidolytic activity with chromogenic peptide substrates of proteinases of the hemostasis system, made it possible to select the A. candidus A4 and A. crustosus A29 strains as promising producers of fibrinolytic proteinases. The proteinases formed by both strains were able to cleave the chromogenic peptide substrates of thrombin, plasmin, factor X, protein C, and urokinase, exhibiting high plasmin-like and thrombin-like activity and not having an activating effect on the proenzymes of the hemostasis system. © 2022, Allerton Press, Inc.
- PublicationRestrictedComparison of COVID-19 Laboratory Diagnosis by Commercial Kits: Effectivity of RT-PCR to the RT-LAMP(Wiley, 2022) ARTIK, YAKUP; Coşgun, Alp B.; Cesur, Nevra P.; Hızel, Nedret; Uyar, Yavuz; Sur, Haydar; AYAN, ALPCoronavirus disease 2019 or COVID-19 caused by novel coronavirus/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) is an ongoing pandemic that has emerging global effects and requires rapid and reliable diagnostic testing. Quantitative reverse transcription-polymerase chain reaction (q-RT-PCR) is the gold standard method for SARS-CoV-2 detections. On the other hand, new approaches remedy the diagnosis difficulties gradually. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) as one of these novel approaches may also contribute to faster and cheaper field-based testing. The present study was designed to evaluate this rapid screening diagnostic test that can give results in 30-45 min and to compare the effectiveness of LAMP to the q-RT-PCR. The 30 randomly chosen patient samples were generated by nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. The sample of quantification cycle (Cq) values was tested using RT-LAMP as well as by conventional q-RT-PCR. The patient samples were tested with four different kits (SENSObiz COVID-19 [SARS-CoV-2] LAMP Assay, the QIAseq DIRECT SARS-CoV-2 kit, Biospeedy SARS-CoV-2 Variant Plus kit, and CoVirion-CV19-2 SARS-CoV-2 OneStep RT-PCR kit) and two different PCR devices (GDS Rotor-Gene Q Thermocycler and Inovia Technologies GenX series). Based on 30 patient samples, the positive/negative ratio (P/N) was 30/0 as Biospeedy and Covirion (positivity 100%), 28/2 as Qiagen kit (positivity 93.3%) for the samples studied on the Inovia device while the same samples on the Rotor-Gene device were 30/0 as Biospeedy and Covirion (positivity 100%), 29/1 as Qiagen kit at the first day (96.7%). On the fifth day, the samples were studied in the Inovia device and the respective results were obtained: 27/3 as Biospeedy (positivity 90%), 16/14 as Qiagen (positivity 53.3%), 28/2 as Covirion kit (positivity 93.3%). When these samples were studied in the Rotor-Gene device, it was 29/1 in Biospeedy and Covirion (positivity 96.7%), 19/11 in the Qiagen kit (positivity 63.3%). When these samples were compared with the LAMP method it was found to be 19/11 (positivity 63.3%) on the first day and 18/12 (positivity 60%) on the fifth day. SARS-CoV-2 test studies will contribute to a proactive approach to the development of rapid diagnosis systems. The LAMP approach presents promising results to monitor exposed individuals and also improves screening efforts in potential ports of entry.
- PublicationOpen AccessGemcitabine in Combination With Epibrassinolide Enhanced the Apoptotic Response in an ER Stress-Dependent Manner and Reduced the Epithelial-Mesenchymal Transition in Pancreatic Cancer Cells(TUBITAK Scientific & Technical Research Council Turkey, 2022) Yerlikaya, Pınar Obakan; Mehdizadehtapeh, Leila; RENCÜZOĞULLARI, ÖZGE; KURYAYEVA, FADINA; ÇEVİKLİ, SENA SEDEF; ÖZAGAR, SEVVAL; ODABAŞ, PINAR SİBEL; TUNÇKOL, SUDE; YETİM, HAKAN; Gürkan, Ajda Çoker; Arışan, Elif DamlaGemcitabine is a broad-spectrum antimetabolite and a deoxycytidine analog recognized as a standard therapy alone or in combination with other antineoplastic agents in the therapy of pancreas cancer. Drug resistance following gemcitabine treatment is a common phenomenon; therefore, combinational therapy models are usually preferred. Pancreatic ductal adenocarcinoma, or pancreas cancer, is the fourth leading cause of cancer-related deaths worldwide. With the increasing incidence of pancreatic cancer every year, the mortality rate is also rising significantly because of late diagnosis, and limited chemotherapy options. Adjuvant chemotherapy after surgical resection is the typical option for the treatment of early pancreatic cancer. Mostly, 5-fluorouracil/leucovorin with irinotecan and oxaliplatin (FOLFIRINOX) and gemcitabine/nab-paclitaxel is used for the prognosis of advanced pancreatic cancer; however, chemoresistance usually occurs limiting the effectiveness of the chemotherapy. Therefore, most of the studies are focused on gemcitabine combination with other drugs to overcome the situation.As an apoptotic agent and a member of brassinosteroids, epibrassinolide (EBR) induces endoplasmic reticulum (ER) stress-dependent cell death in different cancer cells, as shown by our group. In this study, we aimed to enhance the gemcitabine apoptotic effect by EBR combined treatment in pancreatic cancer cells. EBR treatment reduced cell viability and inhibited cell proliferation in PANC-1, MIA PaCa-2, and AsPC-1 cells. Each pancreatic cancer cell gave different responses to the EBR treatment because of different aggressiveness. However, EBR induced apoptosis through increasing ROS generation, which was associated with ER stress in PANC-1 and MIA PaCa-2 cells. Gemcitabine alone reduced the cell viability of each pancreatic cancer cell line; however, combination with EBR led to further induction of apoptotic cell death in each pancreatic cancer cell line. In addition, combined treatment of gemcitabine and EBR further decreased N-cadherin and vimentin expressions, suggesting that epithelial-mesenchymal transition of pancreatic cells is reduced. In conclusion, EBR had therapeutic potential to avoid the gemcitabine-induced side effects during the treatment of pancreatic cancer.