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Article Citation - WoS: 2Citation - Scopus: 2Investigations of Ph-Dependent Dynamic Properties of Ompg-16sl, an Outer Membrane Protein G Mutant by Atr-Ftir Spectroscopy(Elsevier, 2022) Yilmaz, Irem; Korkmaz, FilizIn this paper, the dynamic properties of outer membrane protein G mutant (OmpG-16SL) are investigated with ATR-FTIR spectroscopy. While OmpG-WT has 14 beta-strands in its structure, the mutant is designed to have 16 beta-strands with the intention of creating an enlarged pore. Loop L6 is elongated by introducing six residues, two of which are negatively charged. The solvent accessibility of the OmpG-16SL mutant is compared with WT and a previously reported mutant OmpG-16S by tracking the H-1/H-2 exchange kinetics in acidic and neutral buffer conditions. The exchange kinetics and dynamics in the fast and slow exchange phases are separately investigated using the 2DCOS technique, which enables the tracking of the structural changes at each phase of the exchange process. The results suggest that the mutant OmpG-16SL is equally exposed to buffer in both acidic and neutral pH conditions. Additionally, the time range in the fast phase is very short - one-tenth of that for WT - and most of the exchange is completed in this phase. This fast exchange within minutes is also indicative of the presence of highly flexible and/or unstructured regions. In all, the fast exchange rates independent of the buffer pH justify the assumption that there is an altered interaction among the charged residues, which leads to a steadily-open pore. The role of the side-chain interactions within the pore and between the loops involving the loop L6 is also discussed.Article Citation - WoS: 5Citation - Scopus: 5Molecular/Antigenic Mimicry and Immunological Cross-Reactivity Explains Sars-Cov Autoimmunity(Elsevier, 2025) Adiguzel, Yekbun; Bogdanos, Dimitros P.; Shoenfeld, YehudaCOVID-19 pandemic is over, but its effects on chronic illnesses remain a challenging issue. Understanding the influence of SARS-COV-2-mediated autoimmunity and overt autoimmune disease is of paramount importance, as it can provide a critical mass of information regarding both infection-mediated (and vaccination-induced) autoimmune phenomena in susceptible individuals during the disease course, and short or long-term post-disease sequelae. The high prevalence of organ and non-organ specific autoantibody positivity in patients with COVID-19 led to studies attempting to delineate the origin and the underlying mechanism responsible for their induction nature, identifying novel autoantigens, and the self-epitope sequences which could be the impetus for the initiating autoreactive responses. Herein, we provide a meticulous review of the studies reporting those mimicking sequences that have been experimentally validated, based on the assumption that molecular mimicry and immunological crossreactivity may account for autoantibody development. Most reports are based on bioinformatics approaches, and only a disproportionally small number of studies currently demonstrate immunological crossreactivity. We took the opportunity to further review and searched for the linear human epitope sequences of human, through the epitopes deposited at the Immune Epitope Database. This included an analysis of autoimmune disease as the disease data to comprehensively understand the subject matter. The critical overview of the findings underscore the urgent and immense need for further research to gain a comprehensive understanding of the mechanisms involved and the anticipated appraisal that molecular mimicry and immunological crossreactivity is indeed central to the loss of immunological tolerance during SARS-COV-2 infection.Article Citation - WoS: 6Citation - Scopus: 8Finite Element Analysis of Fgm Dental Crowns Using Phase-Field Approach(Elsevier, 2023) Sait, Ferit; Saeidi, Nazanin; Korkmaz, TuranFunctionally graded materials (FGMs) - categorized in advanced composite materials - are specially designed to reduce the stresses and failure due to material mismatches. Advances in manufacturing techniques have brought FGMs into use in a variety of applications. However, the numerical analysis is still challenging due to the difficulties in simulations of non-homogeneous material domains of complex parts. Presenting a numerical procedure that both facilitates the implementation of material non-homogeneity in geometrically complex mediums, and increases the accuracy of the calculations using a phase-field approach, this study investigates the usage of FGMs in dental prostheses. For this purpose, a porcelain fused to metal (PFM) mandibular first molar FGM crown is simulated and analyzed under the maximum masticatory bite force, and eventually the results are compared to a PFM crown prepared conventionally.Article Citation - WoS: 39Citation - Scopus: 44A Novel Treatment Strategy for Preterm Birth: Intra-Vaginal Progesterone-Loaded Fibrous Patches(Elsevier, 2020) Cam, Muhammet Emin; Hazar-Yavuz, Ayse Nur; Cesur, Sumeyye; Ozkan, Ozan; Alenezi, Hussain; Sasmazel, Hilal Turkoglu; Edirisinghe, Mohan; Turkoglu Sasmazel, HilalProgesterone-loaded poly(lactic) acid fibrous polymeric patches were produced using electrospinning and pressurized gyration for infra-vaginal application to prevent preterm birth. The patches were intravaginally inserted into rats in the final week of their pregnancy, equivalent to the third trimester of human pregnancy. Maintenance tocolysis with progesterone-loaded patches was elucidated by recording the contractile response of uterine smooth muscle to noradrenaline in pregnant rats. Both progesterone-loaded patches indicated similar results from release and thermal studies, however, patches obtained by electrospinning had smaller average diameters and more uniform dispersion compared to pressurized gyration. Patches obtained by pressurized gyration had better results in production yield and tensile strength than electrospinning; thereby pressurized gyration is better suited for scaled-up production. The patches did not affect cell attachment, viability, and proliferation on Vero cells negatively. Consequently, progesterone-loaded patches are a novel and successful treatment strategy for preventing preterm birth.Article Citation - WoS: 5Citation - Scopus: 6Clinic-Oriented Injectable Smart Material for the Treatment of Diabetic Wounds: Coordinating the Release of Gm-Csf and Vegf(Elsevier, 2024) Kinali, Hurmet; Kalaycioglu, Gokce Dicle; Boyacioglu, Ozge; Korkusuz, Petek; Aydogan, Nihal; Vargel, IbrahimChronic wounds are often caused by diabetes and present a challenging clinical problem due to vascular problems leading to ischemia. This inhibits proper wound healing by delaying inflammatory responses and angiogenesis. To address this problem, we have developed injectable particle-loaded hydrogels which sequentially release Granulocyte-macrophage- colony-stimulating-factor (GM-CSF) and Vascular endothelial growth factor (VEGF) encapsulated in polycaprolactone-lecithin-geleol mono-diglyceride hybrid particles. GM-CSF promotes inflammation, while VEGF facilitates angiogenesis. The hybrid particles (200 -1000 nm) designed within the scope of the study can encapsulate the model proteins Bovine Serum Albumin 65 +/- 5 % and Lysozyme 77 +/- 10 % and can release stably for 21 days. In vivo tests and histological findings revealed that in the hydrogels containing GM-CSF/VEGF-loaded hybrid particles, wound depth decreased, inflammation phase increased, and fibrotic scar tissue decreased, while mature granulation tissue was formed on day 10. These findings confirm that the hybrid particles first initiate the inflammation phase by delivering GM-CSF, followed by VEGF, increasing the number of vascularization and thus increasing the healing rate of wounds. We emphasize the importance of multi-component and sequential release in wound healing and propose a unifying therapeutic strategy to sequentially deliver ligands targeting wound healing stages, which is very important in the treatment of the diabetic wounds.Article Citation - WoS: 3Citation - Scopus: 5Subclinical Inflammation Is Associated With Reductions in Muscle Oxygenation, Exercise Capacity and Quality of Life in Adults With Type 2 Diabetes(Elsevier, 2020) Bozdemir-Ozel, Cemile; Arikan, Hulya; Calik-Kutukcu, Ebru; Karaduz, Beyza Nur; Inal-Ince, Deniz; Kabakci, Giray; Dagdelen, SelcukObjectives: Exercise capacity is related to both morbidity and mortality in patients with type 2 diabetes (T2DM). The aim of this study was to investigate the relationship between subclinical inflammation level, exercise capacity, muscle oxygenation and quality of life in T2DM. Methods: This study includes 28 patients with T2DM (mean age, 51.5 +/- 5.0 years; male-to-female ratio, 6:22). Exercise capacity was evaluated using an incremental symptom-limited maximal exercise test on a bicycle ergometer. Muscle oxygenation was investigated using a wearable lactate-measuring device. Diabetes-specific quality of life was assessed using the Diabetes Quality of Life Questionnaire (DQOL). Subclinical inflammation was assessed using C-reactive protein (CRP) levels. Results: CRPlevelwasnegatively correlatedwith peakworkload during the test (r=-0.588, p=0.002), muscle oxygenation (r=-0.465, p= 0.019) and the psychological impact of treatment subscale of the DQOL (r= e0.540, p=0.017), and positively correlated with body mass index (r=0.519, p=0.008), waist circumference (r=0.426, p=0.038) and fat percentage (r=0.573, p=0.004). Therewasnocorrelation betweenCRPand fasting blood glucose or glycated hemoglobin level (p>0.05). Peakworkloadwas inversely related to fat percentage (r=-0.467, p=0.016) and the DQOLworry about the future impact of diabetes subscale (r=-0.501, p=0.021). Conclusions: In our study, subclinical inflammation negatively affected muscle oxygenation, exercise capacity and quality of life independently of glycemic indicators. Our findings suggest that the degree of glycemic control is insufficient to explain lower exercise capacity. Further studies are needed to investigate subclinical inflammation-reducing interventions in T2DM. (C) 2020 Canadian Diabetes Association.Article Citation - WoS: 69Citation - Scopus: 73European Head and Neck Society Recommendations for Head and Neck Cancer Survivorship Care(Elsevier, 2022) Verdonck-de Leeuw, Irma; Hoşal, Ali Şefik; Dawson, Camilla; Licitra, Lisa; Eriksen, Jesper Grau; Hosal, Sefik; Singer, Susanne; Leemans, C. Rene; Hoşal, Ali Şefik; Surgical Sciences; Surgical SciencesSurvivors of head and neck cancer can experience long-term consequences of the cancer and subsequent treatments even after the cancer has resolved. Increasingly clinicians are aware of the social, psychological, financial, and emotional impacts of these cancers, in addition to the support required for the physical symptoms. This review provides recommendations on the long-term management and support required for survivors of head and neck cancer in the European healthcare setting.Article Citation - Scopus: 1The Effect of Folic Acid Supplementation and Folate Deficiency on Embryo Implantation(Elsevier, 2024) Ozdemir, Elif Seda; Bulut, Deniz Irem; Saglam, Atiye Seda Yar; Isgor, Belgin; Elmas, CigdemImplantation is a critical stage of pregnancy, which occurs in a short period of interaction between the receptive endometrium and the embryo. Folic acid (FA) is a synthetic derivative of folate and is recommended as a preconceptional supplement. However, the impact of different doses of FA supplementation and folate deficiency during the early stages of pregnancy requires further investigation. The aim of this study was to investigate the possible effects of FA supplementation and folate deficiency on expression of Estrogen Receptor Alpha (ER-alpha), Vascular Endothelial Growth Factor-A (VEGFA), and Integrin alpha V and beta3 (Integrin alpha V beta 3). A total of 32, 6-8-week old Wistar albino rats were divided into four groups of control, folate-deficiency, low-dose, and highdose FA supplement groups. After five weeks of FA supplementation and folate deficiency model formation, mated rats were sacrificed on the 5th gestational day (GD), and implantation sites were collected. The expression of ER- alpha, VEGFA, and Integrin alpha V beta 3 in the implantation sites were examined with immunohistochemistry and real-time PCR. The results revealed that the mRNA levels of ESR1, VEGFA, and Integrin alpha V and beta 3 were significantly increased in the high-dose FA group and significantly decreased in the folate deficiency group compared to the control group (p < 0.05). Based on these results, it can be concluded that FA supplementation before pregnancy has positive effects on the maintenance of pregnancy, and folate deficiency may lead to implantation disorders.Article Citation - WoS: 16Citation - Scopus: 16Targeted mesoporous silica nanoparticles for improved inhibition of disinfectant resistant Listeria monocytogenes and lower environmental pollution(Elsevier, 2021) Sudagidan, Mert; Yildiz, Gulsah; Onen, Selin; Al, Rabia; Temiz, S. Sevval Nur; Yurt, Mediha Nur Zafer; Ozalp, Veli C.Benzalkonium chloride (BAC) is a common ingredient of disinfectants used for industrial, medical, food safety and domestic applications. It is a common pollutant detected in surface and wastewaters to induce adverse effects on Human health as well as aquatic and terrestrial life forms. Since disinfectant use is essential in combatting against microorganisms, the best approach to reduce ecotoxicity level is to restrict BAC use. We report here that encapsulation of BAC in mesoporous silica nanoparticles can provide an efficient strategy for inhibition of mi-crobial activity with lower than usual concentrations of disinfectants. As a proof-of-concept, Listeria mono-cytogenes was evaluated for minimum inhibitory concentration (MIC) of nanomaterial encapsulated BAC. Aptamer molecular gate structures provided a specific targeting of the disinfectant to Listeria cells, leading to high BAC concentrations around bacterial cells, but significantly reduced amounts in total. This strategy allowed to inhibition of BAC resistant Listeria strains with 8 times less the usual disinfectant dose. BAC encapsulated and aptamer functionalized silica nanoparticles (AptBACNP) effectively killed only target bacteria L. monocytogenes, but not the non-target cells, Staphylococcus aureus or Escherichia coli. AptBACNP was not cytotoxic to Human cells as determined by in vitro viability assays.Article Citation - WoS: 126Citation - Scopus: 156Development of satureja Cuneifolia-loaded< Sodium Alginate/Polyethylene Glycol Scaffolds Produced by 3d-Printing Technology as a Diabetic Wound Dressing Material(Elsevier, 2020) Ilhan, Elif; Cesur, Sumeyye; Guler, Ece; Topal, Fadime; Albayrak, Deniz; Guncu, Mehmet Mucahit; Gunduz, OguzhanAcute wounds are a common health problem, with millions of people affected and decreased granulation tissue formation and vascularization, it is also a big challenge for wound care researchers to promote acute wound healing around the globe. This study aims to produce and characterize Satureja cuneifolia plant extract (SC) blended with sodium alginate (SA) /polyethylene glycol (PEG) scaffolds for the potential treatment of diabetic ulcer. SA/PEG scaffolds were prepared by adding different concentrations (1, 3, and 5 wt%) of PEG to 9 wt% SA. The morphological and chemical composition of the resulting 3D printed composite scaffolds was determined using scanning electron microscopy (SEM) and Fourier transforms infrared spectroscopy (FTIR), respectively. Mechanical and thermal properties, swelling, and degradation behaviours were also investigated. The release kinetics of SC were performed. The antimicrobial analysis was evaluated against Escherichia coli and Staphylococcus aureus strains. 3D printed scaffolds have shown an excellent antibacterial effect, especially against gram-positive bacteria due to the antibacterial SC extract they contain. Furthermore, the cell viability of fibroblast (L929) cells on/within scaffolds were determined by the colourimetric MTT assay. The SA/PEG/SC scaffolds show a great promising potential candidate for diabetic wound healing and against bacterial infections. (c) 2020 Elsevier B.V. All rights reserved.
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