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OpenAccess@IKU İstanbul Kültür Üniversitesi Akademik Açık Erişim Sistemidir. İstanbul Kültür Üniversitesi’nin akademik çıktılarını uluslararası standartlarda dijital ortamda depolamak ve açık erişime sunmak üzere Haziran 2014 yılında kurulmuştur. OpenAccess@IKU, İstanbul Kültür Üniversitesi bünyesinde üretilen makale, sunum, tez, kitap, kitap bölümü, rapor gibi akademik çıktıları içerir.
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Comparison 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, ALP
Coronavirus 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.
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Gemcitabine 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 Damla
Gemcitabine 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.
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UV-induced-OCH3 Rotamerization in a Matrix-Isolated Methoxy-Substituted Ortho-Hydroxyaryl Schiff Base
(Springernature, 2022) Sıdır, İsa; Sıdır, Yadigar Gülseven; Gobi, Sandor; Berber, Halil; ILDIZ, GÜLCE ÖĞRÜÇ; Fausto, Rui
A new methoxy-substituted ortho-hydroxyaryl Schiff base, 4-(3-methoxy-2-hydroxybenzylidene-amino) phenol was synthesized from 4-aminophenol and 2-hydroxy-3-methoxybenzaldehyde in methanol solution and characterized by H-1-NMR, C-13-NMR and infrared spectroscopies and elemental analysis. The compound was isolated in a cryogenic (10 K) argon matrix, and the analysis of the infrared spectrum of the matrix-isolated compound revealed that it corresponds to the E-enol-imine isomeric form, with 3 different conformers being present in the matrix. These conformers share as common structural features the conformation of the free hydroxyl group (trans relatively to the para-substituent of the ring) and the presence of an OH center dot center dot center dot N intramolecular H-bond involving the methoxy-substituted phenol ring and the azomethine bridge, while they differ in the orientation of the methoxy-substituent group. The structures and relative energies of the conformers of the molecule, and relevant barriers for their interconversion were obtained through quantum chemical calculations, which were also used to calculate the infrared spectra of the different forms. Calculations were also carried out for the higher-energy Z-enol-imine and keto-amine forms of the compound. Upon UV (230 nm) irradiation, -OCH3 rotamerization was observed, leading to conversion of the lowest energy conformer, where the methoxy group is aligned with the plane of the ring, into the other two conformers initially present in the matrix, in which the OCH3 group is out-of-the-plane of the ring. As for other phenolic compounds previously studied, spontaneous quantum mechanical tunneling conversion of the cis-OH conformers present in the gas-phase into the three observed conformers was found to take place during matrix deposition.
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Circulating MicroRNA Expression Profiles to Identify a Potential Link Between Prostate Cancer and Obesity
(Elsevier, 2022) Arışan, Serdar; KILBAŞ, PELİN ÖZFİLİZ; RENCÜZOĞULLARI, ÖZGE; Ünsal, Narcin Palavan; Çoker-Gürkan, Ajda; Obakan-Yerlikaya, Pınar; Uysal-Onganer, Pınar; Arışan, Elif Damla
Effective diagnostic methods are needed to apply appropriate treatment strategies in patients with aggressive prostate cancer. From this point of view, risk factors that cause prostate cancer or its aggressiveness should be considered. Obesity is a critical risk factor for triggering prostate cancer's metastatic properties. microRNAs are used as biomarkers in diagnosing cancer and obesity depending on their tissue-specific expression patterns. This study investigates the role of obesity in the metastatic profile of prostate cancer depending on the differential expression signatures of selected miRNAs in prostate cancer and obese patients. The roles of miR-100, miR-141 and miR-145 in prostate cancer and obesity are partially known. However, their potential to become circular biomarkers in the blood is not elucidated. There is no previous data on miR-4463 and miR-653 on prostate cancer and obesity association. In this study, the blood samples were taken and obtained serum from 69 patients of 6 subgroups that consisted of one healthy group and five unhealthy groups based on their different prostate cancer or obesity levels. Five selected miRNA expression analyses (miR-100, miR-141, miR-145, miR-4463, and miR-653) were performed through total RNA isolation, which was confirmed via synthetic cel-miR-39 miRNA. Quantitative Real-Time PCR analyzed the expression levels of selected miRNAs. Data analysis was performed via normalising target miRNA expression levels with cel-miR-39. In this study, we found that the relationship between prostate cancer and obesity was investigated at the molecular level. It was suggested that target miR-100 could be a promising biomarker for non-obese and aggressive prostate cancer patients. miR-145 is a more potential biomarker than miR-141 for non-aggressive and non-obese patients. miR-4463 can be used to predict more prostate cancer patients than obese patients. Lastly, miR-653 can be a biomarker for non-aggressive prostate cancer cells.
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Arteriovenous Fistula Self-Care Behaviors in Patients Receiving Hemodialysis Treatment: Association With Health Literacy and Self-Care Agency
(Sage Publications Ltd., 2022) Bülbül, Elif; Ayvaz, Meryem Yıldız; Yeni, Tuğba; TÜREN, SEVDA; Efil, Sevda
Background: Arteriovenous fistula-related self-care behaviors, self-care agency and health literacy are important for vascular access patency, which is vital in the continuation of hemodialysis treatment. The purpose of this study was to determine the arteriovenous fistula-related self-care behaviors of patients receiving chronic hemodialysis treatment and the relationship between these behaviors and their health literacy and self-care agency levels. Methods: In this descriptive correlational study, the data were collected from 216 chronic hemodialysis patients. Results: The rate of the patients who had good self-care behaviors levels was 83.96%. The sociodemographic variables that were significantly related to AVF-related self-care behaviors were education, employment status and age. It was found that the patients who had had AVF for a longer time had better self-care behaviors regarding their management of symptoms and findings (p < 0.05). As the self-care agency of the patients (r = 0.612, p < 0.001) and their health literacy (r = 0.421, p < 0.001) increased, their AVF-related self-care behaviors also increased. Conclusion: Age, education status, health literacy and self-care agency were identified to affect AVF-related self-care behaviors.
