PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Editorial Editorial: Advancing Biotechnology in Turkiye: a Dedication To All Women(Springer, 2025) Cadirci, Bilge Hilal; Buyukkileci, Ali Oguz; Binay, BarisArticle Trna Wobble Base Modifications and Boric Acid Resistance in Yeast: Boron-Resistant Deletion Mutants Induce the General Amino Acid Control Mechanism and Activate Boron Efflux(NLM (Medline), 2020) Uluisik, I.; С Karakaya, H.; Koc, A.Boric acid is essential for plants and has many vital roles in animals and microorganisms. However, its high doses are toxic to all organisms. We previously screened yeast deletion collections to identify boric acid-resistant and susceptible mutants to identify genes that play a role in boron tolerance. Here, we analyzed boron resistant mutants (elplΔ, elp3Δ, elp6Δ, ncs2Δ, ncs6Δ and ktil2Δ) for their abilities to modulate the general amino acid control system (GAAC) and to induce boron efflux pump ATR1. The mutants analyzed in this study lack the genes that play roles in tRNA Wobble base modifications. We found that all of the boron resistant mutants activated Gcn4-dependent reporter gene activity and increased the transcript level of the ATR1 gene. Additionally, boron resistant cells accumulated less boric acid in their cytoplasm compared to the wild type cells upon boron exposure. Thus, our findings suggested that loss of wobble base modifications in tRNA leads to GAAC activation and ATR1 induction, which in turn reduced intracellular boron levels and caused boron resistance.Article Citation - WoS: 1Citation - Scopus: 1Comparison of Magnetic Seed and Rfid Methods in the Localization of Non-Palpable Breast Lesions(Wolters Kluwer Medknow Publications, 2024) Sanli, Ahmet Necati; Sanli, Deniz E. Tekcan; Golshan, Mehra; Sezgin, Efe; Celik, Varol; Aydogan, FatihBackground: Many methods have been developed for localizing non-palpable breast lesions. This study investigated the success rate and surgical results of the magnetic seed (Magseed) and radiofrequency identification (RFID) method, which are relatively new compared to standard wire-guided localizations. Materials and Methods: 20 simulation (10 Magseed, 10 RFID) models were created using turkey breasts and raisins. Raisins containing magnetic seed and RFID tags were placed on the turkey breast. Sentimag (R) probe was used for the Magseed group, and Faxitron LOCalizer (TM) System device was used in the RFID group. Both methods were evaluated in terms of accuracy in detecting breast lesion localization, operation times, excised tissue weights, total resection volume, surgical margin negativity, and re-excision rates. Results: Lesion localization success in both techniques was 100%. While procedure times were statistically significantly shorter in the Magseed group, incision lengths were shorter in the RFID group (P = 0.013, P = 0.007, respectively). No statistically significant difference was found between the groups for the weight of the removed parts, total resection volume, and surgical margin distance (P > 0.05). Conclusion: In this feasibility study, it was concluded that neither the RFID nor Magseed methods had a significant advantage over each other, in terms of localization detection and surgical margin negativity, and both methods could be used successfully for localization.Article Citation - Scopus: 27Apoptotic Effects of Resveratrol, a Grape Polyphenol, Onimatinib-Sensitive and Resistant K562 Chronic Myeloid Leukemia Cells(2012) Can,G.; Cakir,Z.; Kartal,M.; Gunduz,U.; Baran,Y.Aim: To examine the antiproliferative and apoptotic effects of resveratrol on imatinib-sensitive and imatinib-resistant K562 chronic myeloid leukemia cells. Materials and Methods: Antiproliferative effects of resveratrol were determined by the 3-Bis[2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5- carboxanilide inner salt (XTT) cell proliferation assay. Apoptotic effects of resveratrol on sensitive K562 and resistant K562/IMA-3 cells were determined through changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP), and apoptosis by annexin V-(FITC). Results: The concentrations of resveratrol that inhibited cell growth by 50% ( IC50) were calculated as 85 and 122 μM for K562 and K562/IMA-3 cells, respectively. There were 1.91-, 7.42- and 14.73-fold increases in loss of MMP in K562 cells treated with 10, 50, and 100 μM resveratrol, respectively. The same concentrations of resveratrol resulted in 2.21-, 3.30- and 7.65-fold increases in loss of MMP in K562/IMA-3 cells. Caspase-3 activity increased 1.04-, 2.77- and 4.8-fold in K562 and 1.02-, 1.41- and 3.46-fold in K562/IMA- 3 cells in response to the same concentrations of resveratrol, respectively. Apoptosis was induced in 58.7%-and 43.3% of K562 and K562/IMA-3 cells, respectively, in response to 100 μM resveratrol. Conclusion: Taken together these results may suggest potential use of resveratrol in CML, as well as in patients with primary and/or acquired resistance to imatinib.Article Genetic Factors Associated With Age-Related Macular Degeneration Modulating Plasma Inflammatory Biomarker Levels in Patients With Aids(Taylor & Francis inc, 2024) Sezgin, Efe; Schneider, Michael F.; Hunt, Peter W.; Beck-Engeser, Gabriele; Ambayac, Gabriele C.; Jabs, Douglas A.IntroductionPatients with the acquired immunodeficiency syndrome (AIDS) have an increased prevalence and incidence of intermediate-stage age-related macular degeneration (AMD). Several elevated plasma inflammatory biomarkers are associated with increased incidence of intermediate-stage AMD in this population. We evaluated the association between AMD risk alleles and plasma inflammatory biomarker levels in persons with AIDS.Materials and MethodsCryopreserved plasma specimens of 229 non-Hispanic White and 252 non-Hispanic blacks from the Longitudinal Study of the Ocular Complications of AIDS cohort were assayed for plasma levels of soluble tumor necrosis factor receptor (sTNFR) 2, interleukin (IL)-18, C x 3motif chemokine ligand 1 (CX3CL1), C-reactive protein (CRP), and soluble CD14 (sCD14). Genotyping included AMD-associated variants rs10801553 and rs800292 for complement factor H (CFH) rs9332739 and rs547154 for complement factor 2 (C2), rs2230199 for C3, rs2285714 for CFI, and rs3732379 and rs3732378 for C x 3motif chemokine receptor 1 (CX3CR1).ResultsIn Whites, AMD low-risk CX3CR1 variants (V249I and T280M) were associated with reduced plasma levels of IL-18. In Blacks, AMD low-risk C3 R102G and low-risk CX3CR1 T280M variants were associated with reduced CRP levels.ConclusionsGenetic variants in AMD-associated immune genes may influence AMD-associated systemic plasma inflammatory biomarker levels in patients with AIDS.Article Citation - WoS: 11Türkiye’de Kutanöz Leyşmanyazis Etkeni Leishmania Tropica’da Antimon Direnç Mekanizmasının Belirlenme(Ankara Mikrobiyoloji Derneği, 2020) Özbilgin, Ahmet; Zeyrek, Fadile Yıldız; Güray, Melda Zeynep; Çulha, Gülnaz; Akyar, Işın; Harman, Mehmet; Gündüz, CumhurDünya Sağlık Örgütü, yaklaşık bir milyar insanın endemik bölgelerde risk altında olduğunu, son beş yıl içinde bir milyon kutanöz leyşmanyazis (KL) olgusunun ve yılda yaklaşık 300.000 viseral leyşmanyazis (VL) olgusunun olduğunu bildirmektedir. Her yıl yaklaşık 20.000 kişinin VL’ye bağlı öldüğü bilinmektedir. Türkiye’de Leishmania tropica’nın ve Leishmania infantum’un neden olduğu KL’de yılda 2500 civarında olgu bildirilmektedir. Başta Akdeniz ve Ege Bölgesi illerinde olmak üzere diğer birçok ilde son yıllarda ortaya çıkan olgu ve odaklarda önemli oranda artış görülmesi önümüzdeki yıllarda enfeksiyon hızının yükseleceğini göstermektedir. Ülkemizdeki KL’nin ana etkeni L.tropica olup tedavide meglumin antimonat kullanılmaktadır. Bu çalışmada, antimona dirençli ve dirençli olmayan L.tropica izolatlarının gen ve protein ekspresyonları karşılaştırılarak L.tropica’ya özgü antimon direnç genlerinin saptanması amaçlanmıştır. Ülkemizin Ege, Akdeniz ve Güneydoğu bölgelerinden antimonat direnci bulunmayan 3 KL hastasından elde edilmiş L.tropica izolatlarında, laboratuvar ortamında meglumin antimonata karşı 3 dirençli izolat geliştirilmiştir. Bu izolatların mikroarray yöntemi ile gen ekspresyon değişimleri, 2 boyutlu jel elektroforezi ile protein profilleri ve MALDI-TOF/TOF MS ile ilgili proteinleri tanımlanarak birbirleriyle karşılaştırma yapılmıştır. Antimon tedavisine yanıt vermemiş 10 KL hastasından elde edilmiş L.tropica izolatlarına antimon bileşiklerine yönelik direnç testleri uygulanmış ve direnç gelişiminden sorumlu genlerin ekspresyonlarını saptamak amacıyla kantitatif gerçek zamanlı polimeraz zincir reaksiyonu uygulanmıştır. Ayrıca, protein profilleri karşılaştırılarak antimon direnci olan ve olmayan izolatlardaki protein ekspresyon düzeylerindeki farklılıklar belirlenmiş ve farklılık saptanan proteinlerin tanımlanması gerçekleştirilmiştir. Bu çalışmalar sonucunda, L.tropica izolatlarının antimon bileşiklerine karşı direnç geliştirilen izolatlarında, direnç geliştirmesinde enolaz, “Elongation factor-2 (EF-2)”, “Heat shock protein 70 (HSP 70)”, tripanotyon redüktaz, protein kinaz C ve metalo-peptidaz proteinlerinin rol oynadığı saptanmış ve hastalardan alınan doğal dirençli izolatlarda da benzer ekspresyon değişimi gösterilmiştir. Sonuç olarak, ülkemizdeki L.tropica izolatlarının deneysel olarak çok kısa sürede meglumin antimonata (Glucantime®) karşı direnç kazandığı saptanmıştır. Ülkemizde yaşayan ve yurt dışından ülkemize giriş yapan KL hastalarının yetersiz ve eksik tedavi görmesi durumunda, dirençli suşların ve olgu sayısının hızla artabileceği ve dirençli leyşmanyazis odaklarının oluşabileceği öngörülmektedir.Article Citation - WoS: 12Citation - Scopus: 12Evaluation of Adjuvant Activity of Astragaloside Vii and Its Combination With Different Immunostimulating Agents in Newcastle Disease Vaccine(Academic Press, 2021) Yakuboğulları, Nilgün; Çöven, Furkan Ozan; Cebi, Nusin; Çöven, Fethiye; Çöven, Nejdet; Genç, Rukan; Bedir, ErdalAstragaloside VII (AST-VII), a major cycloartane saponin isolated from Turkish Astragalus species, turned out to be one of the most active metabolites demonstrating Th1/Th2 balanced immune response. As Quillaja saponins are extensively used in adjuvant systems, this study made an attempt to improve AST-VII based adjuvant systems by using different immunostimulatory/delivery agents (monophosphoryllipid A (MPL), Astragalus polysaccharide (APS) and squalene) and to induce cellular and humoral immune response against a viral vaccine. For this purpose, Newcastle Disease vaccine (NDV) was chosen as a model vaccine. Swiss albino mice were immunized subcutaneously with LaSota vaccines in the presence/absence of AST-VII or developed adjuvant systems. AST-VII administration both in live/inactivated LaSota vaccines induced neutralizing and NDV specific IgG, IgG1 and IgG2b antibodies response as well as IL-2 and IL-4 production. APS based delivery systems enhanced the production of neutralizing antibody and the minor augmentation of IFN-? and IL-2 levels. Squalene emulsion (SE) alone or combined with AST-VII were effective in NDV restimulated splenocyte proliferation. As a conclusion, AST-VII and AST-VII containing adjuvant systems demonstrated Th1/Th2 balanced antibody and cellular immune responses in NDV vaccines. Thus, these systems could be developed as vaccine adjuvants in viral vaccines as alternative to saponin-based adjuvants.Article Citation - WoS: 5Citation - Scopus: 5Evaluation of Liposomal and Microbubbles Mediated Delivery of Doxorubicin in Two-Dimensional (2d) and Three-Dimensional (3d) Models for Breast Cancer(Galenos Publishing House, 2021) Aydın,M.; Özdemir,E.; Altun,Z.; Kılıç,S.; Aktaş,S.Objective: Liposomal cancer treatment strategies are useful in removing the side effects that were the main concern in recent years. In this study, we prepared microbubble (MBs) conjugated with DOX-loaded liposomes (DOX-loaded MBs) and investigated their effectiveness in in vitro breast cancer cells in two dimensions (2D) and three dimensions (3D). Materials and Methods: With this aim, breast cancer cells with different features (4T1, MDA-MB231, MCF-7) were growth in 2D and 3D dimensions. The cytotoxic and cell death effects under different conditions, durations and doses were evaluated with WST-1, trypan-blue, colony counts. Apoptotic effects were investigated with flow cytometric Annexin-V-PI and immunohistochemical (Ki-67, caspase 3, 8, 9) methods. Results: After free DOX and LipoDOX were applied, the proliferation index of three cell lines reduced. Intrinsic and extrinsic apoptotic pathways were activated in both 2D and 3D models. However, this effect was observed at lower levels in the 3D model due to the difficulty of diffusion of DOX into the spheroids. Additionally, the suitability of the 3D model for breast cancer cells was supported by formation of ductus-like structures and spheroids. Cell deaths were not observed significantly with the DOX-loaded microbubbles due to rising of MBs to the surface and not reaching spheroids held in matrigel of 3D model. Conclusion: DOX and LipoDOX showed anti-proliferative and apoptosis-inducing effects in breast cancer cells. However, these effects indicated variability depending on the cell lines and 2D or 3D model types. ©Copyright 2021 by the the Turkish Federation of Breast Diseases Societies.Article Citation - WoS: 3Citation - Scopus: 4Comparison of the Effects of Statins on A549 Nonsmall-Cell Lung Cancer Cell Line Lipids Using Fourier Transform Infrared Spectroscopy: Rosuvastatin Stands Out(Wiley, 2021) Aksoy, Hatice Nurdan; Ceylan, ÇağatayStatins are commonly prescribed antilipidemic and anticholesterol class of drugs. In addition to their major role, they have been found to have anticancer effects on in vitro, animal and clinical studies. The aim of this study was to investigate the effects of six different statins (rosuvastatin, pravastatin, simvastatin, lovastatin, fluvastatin, and atorvastatin) on A549 cancer cells lipids by Fourier transform infrared (FTIR) spectroscopy. Proliferation tests were carried out to detect the half-maximal inhibitory concentrations (IC50) of each statin on A549 cells. The IC50 values were 50 mu M for simvastatin, 150 mu M for atorvastatin and pravastatin, and 170 mu M for fluvastatin, 200 mu M for rosuvastatin and lovastatin on A549 cells. No correlation was found between the antiproliferative effects of the statins and lipid-lowering effect. The cells were treated with IC5, IC10, and IC50 values of each statins concentration and lipid extracts were compared using FTIR spectroscopy. The results indicated that different statins had different effects on the lipid content of A549 cells. The FTIR spectra of the lipid exctracts of statin-treated A549 cells indicated that the value of hydrocarbon chain length, unsaturation index, oxidative stress level, and phospholipid containing lipids increased except for rosuvastatin-treated A549 cells. In addition, rosuvastatin significantly lowered cholesterol ester levels. In conclusion, the contrasting effects of rosuvastatin should be further investigated.Article Citation - WoS: 2Türkiye’de Kutanöz Leyşmanyazis Hastalarından Elde Edilen Leishmania İzolatlarındaki Farklılıklar ve Bunların Fare Modeline Klinik Yansıması(Ankara Microbiology Society, 2020) Özbilgin, Ahmet; Çulha, Gülnaz; Güray, Melda Zeynep; Zeyrek, Fadile Yıldız; Akyar, Işın; Toz, Seray; Gündüz, CumhurAlthough asexual reproduction has been attributed to Leishmania species, genetic exchange has recently been demonstrated, which helped emerging of hybrid isolates. Situated on the crossroads between three continents, Leishmania hybrids may be present in Turkey. In Turkey, visceral leishmaniasis caused by Leishmania infantum is less common, while cutaneous leishmaniasis (CL) caused by Leishmania tropica and L.infantum could reach 2500 reported cases a year. Our aim was to investigate genetic variability of local Leishmania species and presence of hybrid Leishmania strains in Turkey. Twenty CL patients from Sanliurfa and Hatay, where only L.tropica and both L.tropica and L.infantum cause CL, respectively, were registered equally. All isolates were assessed with real-time polymerase chain reaction (Rt-PCR), isoenzyme analysis, gene sequencing, two-dimensional gel electrophoresis (2D-PAGE) and MALDI-TOF/TOF-MS followed by in vivo analyses on mouse model. Identification of differentially expressed proteins was performed. These proteins were confirmed by sequence analysis. All isolates from Sanliurfa were found to be L.tropica which caused cutaneous infection in mice. However, one of 10 isolates from Hatay was found as Leishmania major which caused cutaneous infection. Five isolates were found as L.tropica with Rt-PCR and gene sequencing, one of which had one different protein from the reference L.tropica strain and caused cutaneous infection. Four of the five isolates had five different proteins compared to reference strain and caused both cutaneous and visceral infections. Remaining four isolates showed double melting curves in Rt-PCR, which were concordant with L.tropica and L.infantum. Their sequencing and isoenzyme analyses indicated them as L.infantum. They had six different proteins compared to reference L.infantum strain and caused cutaneous and visceral infections. It is concluded that the isolates with different proteins were hybrid Leishmania species. In the present study, outcomes of the proteomics, genomics, clinical manifestations and tissue tropism on animal models were evaluated together for the first time. In addition to L. tropica and L.infantum, L.major was identified as a causative agent for CL and hybrids of Linfantum/tropica were also shown to be present.
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