WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 1Citation - Scopus: 1Lithium Treatment Rescues Dysfunctional Autophagy in the Cell Models of Tay-Sachs Disease(Academic Press Inc., 2024) Basirli,H.; Can,M.; Sengul,T.; Seyrantepe,V.Tay-Sachs disease is a rare lysosomal storage disorder (LSD) caused by a mutation in the HexA gene coding β-hexosaminidase A enzyme. The disruption of the HexA gene causes the accumulation of GM2 ganglioside resulting in progressive neurodegeneration in humans. Surprisingly, Hexa−/− mice did not show neurological phenotypes. Our group recently generated a murine model of Tay-Sachs disease exhibiting excessive GM2 accumulation and severe neuropathological abnormalities mimicking Tay-Sachs patients. Previously, we reported impaired autophagic flux in the brain of Hexa/-Neu3−/− mice. However, regulation of autophagic flux using inducers has not been clarified in Tay-Sachs disease cells. Here, we evaluated the effects of lithium treatment on dysfunctional autophagic flux using LC3 and p62 in the fibroblast and neuroglia of Hexa−/-Neu3−/− mice and Tay-Sachs patients. We discovered the clearance of accumulating autophagosomes, aggregate-prone metabolites, and GM2 ganglioside under lithium-induced conditions. Our data suggest that targeting autophagic flux with an autophagy inducer might be a rational therapeutic strategy for the treatment of Tay-Sachs disease. © 2024 Elsevier Inc.Article Citation - WoS: 6Citation - Scopus: 6Biomolecular Fingerprints of the Effect of Zoledronic Acid on Prostate Cancer Stem Cells: Comparison of 2d and 3d Cell Culture Models(Academic Press Inc., 2024) Güler,G.; Acikgoz,E.; Mukhtarova,G.; Oktem,G.Revealing the potential of candidate drugs against different cancer types without disrupting normal cells depends on the drug mode of action. In the current study, the drug response of prostate cancer stem cells (PCSCs) to zoledronic acid (ZOL) grown in two-dimensional (2D) and three-dimensional (3D) culture systems was compared using Fourier transform-infrared (FT-IR) spectroscopy which is a vibrational spectroscopic technique, supporting by biochemical assays and imaging techniques. Based on our data, in 2D cell culture conditions, the ZOL treatment of PCSCs isolated according to both C133 and CD44 cell surface properties induced early/late apoptosis and suppressed migration ability. The CD133 gene expression and protein levels were altered, depending on culture systems. CD133 expression was significantly reduced in 2D cells upon ZOL treatment. FT-IR data revealed that the integrity, fluidity, and ordering/disordering states of the cell membrane and nucleic acid content were altered in both 2D and 3D cells after ZOL treatment. Regular protein structures decrease in 2D cells while glycogen and protein contents increase in 3D cells, indicating a more pronounced cytotoxic effect of ZOL for 2D cells. Untreated 3D PCSCs exhibited an even different spectral profile associated with IR signals of lipids, proteins, nucleic acids, and glycogen in comparison to untreated 2D cells. Our study revealed significant differences in the drug response and cellular constituents between 2D and 3D cells. Exploring molecular targets and/or drug-action mechanisms is significant in cancer treatment approaches; thus, FT-IR spectroscopy can be successfully applied as a novel drug-screening method in clinical research. © 2024 Elsevier Inc.Article Citation - WoS: 17Citation - Scopus: 21Utilization of Stalk Waste Separated During Processing of Sun-Dried Figs (ficus Carica) as a Source of Pectin: Extraction and Determination of Molecular and Functional Properties(Academic Press Inc., 2022) Çavdaroğlu, Elif; Yemenicioğlu, AhmetThis study aimed the utilization of fig stalk waste as an alternative pectin source. For this purpose, the characteristics of extracted stalk waste pectin (SP) were compared with those of citrus pectin (CP) and pectin extracted from defected substandard whole sun-dried figs (FP). The SP had a higher extraction yield (11.7%) than FP (9.4%). The galacturonic acid content and degree of esterification of SP (32.3 and 50.1%) were higher than those of FP (19.9 and 38.8%), but lower than those of CP (79.3 and 56.2%), respectively. The SP and CP had different sugar compositions (D-glucose, L-rhamnose, D-galactose and L-arabinose) and weight average molecular weights, but similar FTIR profiles. The SP showed almost 1.9 and 1.6-fold higher Trolox equivalent antioxidant capacity (TEAC), and 2.7 and 2.0-fold higher water absorption capacity than CP and FP, respectively. SP at 3% (w/w) showed the second highest viscosity after CP and the highest emulsion stability. Gels of SP and CP at 1.75–3% range had similar firmness, but SP formed more fracturable gels than CP. Sun-dried fig stalk waste is a better source of pectin than defected substandard whole sun-dried figs. The SP could be utilized to develop functional food with alternative textural and rheological properties.Article Citation - WoS: 5Citation - Scopus: 9Antilisterial Effects of Lysozyme-Nisin Combination at Temperature and Ph Ranges Optimal for Lysozyme Activity: Test of Key Findings To Inactivate Listeria in Raw Milk(Academic Press Inc., 2021) Sözbilen, Gözde Seval; Yemenicioğlu, AhmetThis study aimed to determine antilisterial potential of lysozyme (LYS)-nisin (NIS) combination at temperatures and pHs optimal for LYS activity. Tests in buffers at pH 4.5 and 6.0 showed that heating at 50 or 60 °C combined with LYS-NIS caused higher Listeria innocua inactivation (- 6.2 to >6.6 log) than heating alone (- 0.05 to 5.5 log), or heating combined with LYS (- 4.34 to 6.0 log) or NIS (3.9 to >6.6). The antimicrobial performance of LYS-NIS in buffer at 50 °C was not pH-dependant (5.8–5.9 logs) while heating at 60 °C with LYS-NIS at pH 6.0 (>6.6 logs) caused higher Listeria reduction than that at pH 4.5 (5.7 logs). Heating at 50 °C for 45 min alone or in combination with LYS-NIS caused 0 and 5.5 logs Listeria reduction in milk, respectively. In contrast, Listeria inactivation in milk at 60 °C occurred mainly by heat (5.5 logs) with limited contribution of LYS and/or NIS. Milk heated at 50 °C maintained 73% of NIS and 63% of LYS activity. Application of LYS-NIS at 50 °C provides an opportunity to improve milk safety with less destruction of milk enzyme and microbial flora necessary to obtain desired ripening periods, and aroma and flavour in traditional cheeses. © 2020 Elsevier LtdConference Object Mass Spectrometry and Thin Layer Chromatography Analysis of Brain Gangliosides in Tay-Sachs Disease Mouse Models(Academic Press Inc., 2014) Seyrantepe, Volkan; Timur, Zehra; Marsching, C.; Sandhoff, Roger[No abstract available]Article Citation - WoS: 3Citation - Scopus: 3Reconstruction of Generalized Impedance Functions for 3d Acoustic Scattering(Academic Press Inc., 2019) Ivanyshyn Yaman, OlhaWe consider the inverse obstacle scattering problem of determining both of the surface impedance functions from far field measurements for a few incident plane waves at a fixed frequency. The reconstruction algorithm we propose is based on an iteratively regularized Newton-type method and nonlinear integral equations. The mathematical foundation of the method is presented and the feasibility is illustrated by numerical examples. (C) 2019 Elsevier Inc. All rights reserved.Article Citation - WoS: 26Citation - Scopus: 26Multi-Route - Multi-Pathway Exposure To Trihalomethanes and Associated Cumulative Health Risks With Response and Dose Addition(Academic Press Inc., 2019) Genişoğlu, Mesut; Ergi Kaytmaz, Ceyda; Sofuoğlu, Sait CemilCumulative health risk estimation for exposure to mixtures is a current issue, which would present a useful tool for environmental and public health management. Cumulative risks were estimated with response and dose addition methods for individual multi-route - multi-pathway exposure to trihalomethanes and associated carcinogenic toxic risks in Izmir, Turkey. Exposure levels were estimated for ingestion, dermal, and inhalation routes using measured tap water and bottled water THM concentrations. Drinking, showering, hand and dish washing were the considered pathways. THM concentrations in air during the showering were modeled with two-resistance theory using tap water concentration data. The estimated carcinogenic risk levels for ingestion route were in the range of safe (< 10(-6)) to low priority (< 10(-4)), for dermal route all were in the safe zone (< 10(-6)), and for inhalation route were in the range of safe to high priority (> 10(-4)) zones, indicating ingestion and inhalation routes were of similar significance ahead of dermal exposure. Cumulative carcinogenic risks of THM compounds were estimated using simple (response) addition and dose addition using cumulative relative potency factor (CRPF) methods. CRPF method estimated the risks at lower levels compared to the simple addition, which originated from the use two different risk factor values for the index chemical in the method. Cumulative chronic-toxic risks were also assessed, rendering below the threshold risk levels for all routes. This study showed that multi-route - multi-pathway exposure assessment and cumulative risk assessment should together be considered for better environmental and public health management.Article Citation - WoS: 15Citation - Scopus: 16A Mode Shape Assembly Algorithm by Using Two Stage Bayesian Fast Fourier Transform Approach(Academic Press Inc., 2019) Hızal, Çağlayan; Turan, Gürsoy; Aktaş, Engin; Ceylan, HasanOperational modal analysis may require identifying global modal shapes by using multiple setup measurements. For this purpose, various algorithms have been developed which make use of the Bayesian approach to estimate the global mode shapes. The main motivation of the available Bayesian approaches is based on the estimation of the optimal global mode shape vector directly from Fast Fourier Transform data or assembling the local mode shapes that are identified in the individual setups by using Gaussian approximation. In this study, the two-stage Bayesian Fast Fourier Transform Approach which is originally applied to single setups is implemented to multiple setup problems for well separated modes. Analytically it is shown that the resulting formulation is the same for the mode shape assembly by using the Gaussian approximation. In addition, the weights of individual setups in the global mode shape vector is analytically calculated which depend on the Hessian matrix for local mode shapes. To validate the proposed methodology, a numerical example that considers setup-to-setup variability of modal signal-noise ratios is presented. For comparison purposes a ten-story shear frame model is experimentally investigated, and the measurements of a benchmark bridge structure are considered in the verification of the current procedure. (C) 2019 Elsevier Ltd. All rights reserved.Article Citation - WoS: 41Citation - Scopus: 43Chloride or Sulfate? Consequences for Ozonation of Textile Wastewater(Academic Press Inc., 2019) Öktem, Yalçın Aşkın; Yüzer, Burak; Aydın, Muhammed Iberia; Ökten, Hatice Eser; Meriç, Süreyya; Selçuk, HüseyinOzonation of chloride-rich textile wastewater is a common pretreatment practice in order to increase biodegradability and therefore meet the discharge limits. This study is the first to investigate ozone-chloride/bromide interactions and formation of hazardous adsorbable organic halogens (AOX) in real textile wastewater. Initially effect of ozonation on chloride-rich real textile wastewater samples were investigated for adsorbable organic halogens (AOX) formation, biodegradability and toxicity. After 15 min of ozonation, maximum levels of chlorine/bromine generation (0.3 mg/l) and AOX formation (399 mg/l) were reached. OUR and SOUR levels both increased by approximately 58%. Daphnia magna toxicity peaked at 100% for 10 min ozonated sample. Considering adverse effects of ozonation on chloride-rich textile industry effluents, we proposed replacement of NaCl with Na2SO4. Comparative ozonation experiments were carried out for both chloride and sulfate containing synthetic dyeing wastewater samples. Results showed that use of sulfate in reactive dyeing increased biodegradability and decreased acute toxicity. Although sulfate is preferred over chloride for more effective dyeing performance, the switch has been hampered due to sodium sulfate's higher unit cost. However, consideration of indirect costs such as contributions to biodegradability, toxicity, water and salt recovery shall facilitate textile industry's switch from chloride to sulfate.Article Citation - WoS: 24Citation - Scopus: 35Physicochemical and Rheological Properties of Rice-Based Gluten-Free Blends Containing Differently Treated Chickpea Flours(Academic Press Inc., 2018) Kahraman, Gökçen; Harsa, Şebnem; Lucisano, Mara; Cappa, CarolaThis study focused on the evaluation of the physicochemical and rheological properties of chickpea flours and blends obtained by partially substituting rice flour (25 g/100 g) with raw, roasted and dehulled chickpea flour. The characteristics of the resultant doughs were evaluated. In comparison with rice flour, blends containing chickpea flours exhibited high protein and fat content, a reduced retrogradation tendency (setback values of 404–415 vs. 479 Brabender Unit) and a higher foaming capacity and stability, which can be beneficial for their use in baked food formulations. However, roasting decreased foaming capacity and stability. Even if the rheofermentographic test evidenced a slight reduction in dough development, high CO2 retention capacity (≥ 98%) and similar-to-lower leavening times were observed for doughs containing chickpea flours. Incorporating chickpea flours also caused an increase in the viscous and elastic moduli of rice-based doughs, resulting in a good structuring of the dough. The results of this study indicated that chickpea flours could be used as a healthy ingredient in gluten-free rice-based formulations.