OpenAIRE Collection / OpenAIRE Koleksiyonu

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Citation - WoS: 48
Citation - Scopus: 48
5-Fluorouracil Signaling Through a Calcium-Calmodulin Pathway Is Required for P53 Activation and Apoptosis in Colon Carcinoma Cells
(Nature Publishing Group, 2013-09) Can, G.; Akpınar, B.; Baran, Yusuf; Zhivotovsky, B.; Olsson, M.; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
5-Fluorouracil (5-FU) is an anti-metabolite that is in clinical use for treatment of several cancers. In cells, it is converted into three distinct fluoro-based nucleotide analogs, which interfere with DNA synthesis and repair, leading to genome impairment and, eventually, apoptotic cell death. Current knowledge states that in certain cell types, 5-FU-induced stress is signaling through a p53-dependent induction of tumor necrosis factor-receptor oligomerization required for death-inducing signaling complex formation and caspase-8 activation. Here we establish a role of calcium (Ca 2+) as a messenger for p53 activation in response to 5-FU. Using a combination of pharmacological and genetic approaches, we show that treatment of colon carcinoma cells stimulates entry of extracellular Ca 2+ through long lasting-type plasma membrane channels, which further directs posttranslational phosphorylation of at least three p53 serine residues (S15, S33 and S37) by means of calmodulin (CaM) activity. Obstructing this pathway by the Ca 2+ -chelator BAPTA (1,2-bis(o-aminophenoxy)ethane- N,N,N',N'-tetraacetic acid) or by inhibitors of CaM efficiently reduces 5-FU-induced caspase activities and subsequent cell death. Moreover, ectopic expression of p53 S15A in HCT116 p53 -/- cells confirmed the importance of a Ca 2+ -CaM-p53 axis in 5-FU-induced extrinsic apoptosis. The fact that a widely used therapeutic drug, such as 5-FU, is operating via this pathway could provide new therapeutic intervention points, or specify new combinatorial treatment regimes. © 2013 Macmillan Publishers Limited.
Citation - WoS: 6
Citation - Scopus: 9
Adaptive Limited Feedback Links for Cooperative Multi-Antenna Multicell Networks
(Springer Verlag, 2014) Özbek, Berna; Ruyet, Didier Le; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
The overall performance of cooperative networks is quite sensitive to channel state information (CSI) of serving and interfering base stations (BSs) and affected strongly by quality of limited feedback links. In this paper, we propose two adaptive limited feedback strategies for intercell interference cancelation in multi-antenna multicell networks. The first proposed strategy is developed to improve average multicell capacity assuming a fixed rate feedback link. This algorithm is based on adaptation of the number of bits to quantize CSI of serving and interfering BSs according to transmitter power and location of the user in its own cell. The second proposed strategy is designed in a way to increase average capacity of cell-edge users assuming an adaptive rate feedback link. This algorithm is based on the idea of allocating more bits to quantize CSI of users at cell-edge regions while allocating less bits for users near the serving BS. We illustrate performance of the proposed feedback links for downlink cooperative multi-antenna multicell networks in wireless channels.
Citation - WoS: 4
Citation - Scopus: 7
Adaptive Reduced Feedback Links for Distributed Power Allocation in Multicell Miso-Ofdma Networks
(IEEE Computer Society, 2014-04) Özbek, Berna; Le Ruyet, Didier; Pischella, Mylene; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
For multi-antenna Orthogonal Frequency-Division Multiple Access (OFDMA) based multicell networks, the channel state information (CSI) of all users is required to share among base stations in order to perform distributed power allocation. However, the amount of feedback increases with the number of users, base stations, subcarriers and antennas. Therefore, it is important to perform a selection at the user side to reduce the feedback load and the complexity of resource allocation. In this letter, we propose adaptive reduced feedback links by choosing the users based on their approximate signal to interference noise ratio (SINR) and their locations in the cell to satisfy users' rate constraints. We illustrate the performance results of reduced feedback links by employing distributed resource allocation with link adaptation.
Alteration of Protein Localization and Intracellular Calcium Content Due To Connexin26 D50a and A88v Mutations
(Türk Biyokimya Derneği, 2017-04) Aypek, Hande; Meşe, Gülistan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
Introduction: Connexins (Cx) play essential roles in cellular homeostasis by forming gap junctions and non-junctional hemichannels. In vitro characterization of Cx26 mutations causing keratitis-ichthyosis-deafness (KID) syndrome, were shown to form leaky hemichannels. The molecular/ cellular mechanisms affected by aberrant hemichannels have recently been elucidated. Here, we further wanted to characterize Cx26 KID syndrome mutations, D50A and A88V, which were shown to form aberrant hemichannels and remained unaddressed in the literature. Methods: Neurobiotin uptake assay in HeLa and N2A cells transfected with Cx26-WT, D50A or A88V verified the presence of aberrant hemichannels and immunofluorescent staining with fluorescent microscopy determined cellular localization of Cx26. Finally, intracellular calcium content was examined by using calcium indicator, Fluo-3AM, and flow cytometer. Results: Cx26-D50A and A88V mutations prevented the formation of gap junction plaques at cell-cell appositions and mutant proteins were observed to localize to the Golgi apparatus. Further, comparison of intracellular calcium content showed an increase in calcium amount in cells containing Cx26-D50A and A88V relative to Cx26-WT. Conclusion: Retention of Cx26 in the Golgi apparatus and alteration in the intracellular calcium content due to KID syndrome mutations may influence various cellular processes that might contribute to development of epidermal phenotypes.
Citation - WoS: 14
Citation - Scopus: 16
Altered Cellular Localization and Hemichannel Activities of Kid Syndrome Associated Connexin26 I30n and D50y Mutations
(BioMed Central Ltd., 2016) Aypek, Hande; Meşe Özçivici, Gülistan; Bay, Veysel; Meşe Özçivici, Gülistan; Meşe, Gülistan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
Background: Gap junctions facilitate exchange of small molecules between adjacent cells, serving a crucial function for the maintenance of cellular homeostasis. Mutations in connexins, the basic unit of gap junctions, are associated with several human hereditary disorders. For example, mutations in connexin26 (Cx26) cause both non-syndromic deafness and syndromic deafness associated with skin abnormalities such as keratitis-ichthyosis-deafness (KID) syndrome. These mutations can alter the formation and function of gap junction channels through different mechanisms, and in turn interfere with various cellular processes leading to distinct disorders. The KID associated Cx26 mutations were mostly shown to result in elevated hemichannel activities. However, the effects of these aberrant hemichannels on cellular processes are recently being deciphered. Here, we assessed the effect of two Cx26 mutations associated with KID syndrome, Cx26I30N and D50Y, on protein biosynthesis and channel function in N2A and HeLa cells. Results: Immunostaining experiments showed that Cx26I30N and D50Y failed to form gap junction plaques at cell-cell contact sites. Further, these mutations resulted in the retention of Cx26 protein in the Golgi apparatus. Examination of hemichannel function by fluorescent dye uptake assays revealed that cells with Cx26I30N and D50Y mutations had increased dye uptake compared to Cx26WT (wild-type) containing cells, indicating abnormal hemichannel activities. Cells with mutant proteins had elevated intracellular calcium levels compared to Cx26WT transfected cells, which were abolished by a hemichannel blocker, carbenoxolone (CBX), as measured by Fluo-3 AM loading and flow cytometry. Conclusions: Here, we demonstrated that Cx26I30N and D50Y mutations resulted in the formation of aberrant hemichannels that might result in elevated intracellular calcium levels, a process which may contribute to the hyperproliferative epidermal phenotypes of KID syndrome.
Citation - WoS: 4
Citation - Scopus: 4
Analytical Solution of Micro-/Nanoscale Convective Liquid Flows in Tubes and Slits
(Springer, 2017) Kalyoncu, Gülce; Barışık, Murat; 03.10. Department of Mechanical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
Analytical solutions examining heat transport in micro-/nanoscale liquid flows were developed. Using the energy equation coupled with fully developed velocity, we solved developing temperature profiles with axial conduction and viscous dissipation terms. A comprehensive literature review provided the published range of velocity slip and temperature jump conditions. While molecular simulations and experiments present constant slip and jump values for a specific liquid/surface couple independent of confinement size, non-dimensional forms of these boundary conditions were found appropriate to calculate non-equilibrium as a function of flow height. Although slip and jump conditions are specific for each liquid/surface couple and hard to obtain, we proposed modeling of the slip and jump as a function of the surface wetting, in order to create a general, easy to measure methodology. We further developed possible correlations to calculate jump using the slip value of the corresponding surface and tested in the results. Fully developed Nu showed strong dependence on slip and jump. Heat transfer stopped when slip and jump coefficients became higher than a certain value. Strong variation of Nu in the thermal development length was observed for low slip and jump cases, while an almost constant Nu in the flow direction was found for high slip and jump coefficients. Variation of temperature profiles was found to dominate the heat transfer through the constant temperature surface while surface and liquid temperatures became equal at heat transfer lengths comparable with confinement sizes for no-dissipation cases. In case of non-negligible heat dissipation, viscous heating dominated the Nu value by enhancing the heating while decreasing the heat removal in cooling cases. Implementation of proposed procedure on a micro-channel convection problem from a micro-fluidics application showed the dominant effect of the model defining the slip and jump relationship. Direct use of kinetic gas theory resulted in an increase of Nu by an increase in non-equilibrium, while models developed from published liquid slip and jump values produced an opposite behavior.
Citation - WoS: 2
Citation - Scopus: 1
Ankos Publisher Application System and Its Impact on the E-Resource Evaluation Process
(Taylor and Francis Ltd., 2013-02-20) Bulut, Burcu; Uğur, Handan; Gürdal, Gültekin; Holt, İlkay; Çukadar, Sami; Akbayrak, Emre H.; Çelebi, Mustafa K.; 07. Library; 01. Izmir Institute of Technology
The Publisher Application System(PAS) is aWeb-based archiving and online evaluation systemdeveloped by the Database Evaluation Group (DEG), one of the working groups formed within the Anatolian University Libraries Consortium (ANKOS). The DEG was formed in 2008 to inquire and evaluate e-resources suited to the needs of the consortium; to follow up similar consortial activities worldwide as well as developments in connection with the scientific publishing industry; and to determine, implement, and improve pricing models in accordance with the prevailing economic, legal, and academic system. Development of the PAS was essential to ensure standardization and sustainability towards a more detailed and effective analysis of e-resources qualifying for evaluation by ANKOS. The PAS played an important part not only in establishing and defining the workflow of the DEG, but also in creating an archive of both the e-resources submitted to the consortium and the applicant publishers/agents submitting these resources. This article outlines the process that started with the foundation of the DEG through the formation of the PAS as well as the present setup of the system. It is also hoped that this case study will have a positive contribution to the processes being followed by the persons and the groups engaged in similar activities.
Drıver Rehberi 2.0: İçerik Sağlayıcılar için Rehber -- Oaı-pmh ile Metinsel Bilgi Kaynakların Keşfi
(OpenAIRE, 2014-09-09) OpenAIRE; Gürdal, Gültekin; Vanderfeesten, Maurice; Summann, Friedrich; Slabbertje, Martin; Yazıcı, Banu; Çelik, Sönmez; 07. Library; 01. Izmir Institute of Technology; Gürdal, Gültekin
Genel anlamda iletişim için B kişisinin A kişinin söylediğini anlayabilmesi çok önemlidir. Ortak bir anlayış için ortak bir zemin, nesnelerin anlamları konusunda farkındalık sağlayan temel bir sözlüğe ihtiyaç vardır. Bu noktadan sonra kişi akıl yürütmeye başlayabilir. Açık erişim sistemleri akademik iletişimi desteklemek için aynı dili konuşmalıdır. Bu aynı zamanda ortak bir zemin yaratmak için de gereklidir. Teknik anlamda, “konuşabilirlik” sağlayarak ortak bir zemin yaratırız. Konuşabilirlik farklı katmanlarda yürütülebilir. DRIVER Rehberinde konuşabilirlik, söz dizimsel (OAI-PMH kullanımı ve OAI_DC kullanımı) ve anlamsal (terminolojinin kullanımı) olmak üzere iki temel yolla elde edilmeye çalışılmıştır.
Citation - WoS: 11
Citation - Scopus: 12
The Extended Graetz Problem for Micro-Slit Geometries; Analytical Coupling of Rarefaction, Axial Conduction and Viscous Dissipation
(Elsevier Ltd., 2016-12) Kalyoncu, Gülce; Barışık, Murat; 03.10. Department of Mechanical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
In order to support the recent MEMS and Lab-on-a-chip technologies, we studied heat transport in micro-scale slit channel gas flows. Since the micro convection transport phenomena diverges from conventional macro-scale transport due to rarefaction, axial conduction and viscous heating, an accurate understanding requires a complete coupling of these effects. For such cases, we studied heat transfer in hydrodynamically developed, thermally developing gas flows in micro-slits at various flow conditions. The analytical solution of the energy equation considered both the heat conduction in the axial direction and heat dissipation of viscous forces. Furthermore, updated boundary conditions of velocity slip and temperature jump were applied based on Knudsen number of flow in order to account for the non-equilibrium gas dynamics. Local Nusselt number (Nu) values were calculated as a function of Peclet (Pe), Knudsen (Kn) and Brinkman (Br) numbers which were selected carefully according to possible micro-flow cases. Strong variation of Nu in thermal development length was found to dominate heat transfer behavior of micro-slits with short heating lengths for early slip flow regime. For this instance, influence of axial conduction and viscous dissipation was equally important. On the other hand, high Kn slip flow suppressed the axial conduction while viscous heating in a small surface-gas temperature difference case mostly determined the fully developed Nu and average heat transfer behavior as a function of Kn value.
Interactions of Cancer Cells and Macrophages on the Egf-Egfr Axis: Chemotaxis, Haptotaxis or Direct Contact?
(Izmir Institute of Technology, 2017-06) Önal, Sevgi; Pesen Okvur, Devrim; Bulmuş Zareie, Esma Volga; 04.03. Department of Molecular Biology and Genetics; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of Technology
Breast cancer cells (BCC) and macrophages are known to interact via epidermal growth factor (EGF) produced by macrophages and colony stimulating factor-1 (CSF-1) produced by BCC. Despite contradictory findings, this interaction is perceived as a paracrine loop. Yet, the underlying mechanism of interaction remains unclear. Here, we investigated interactions of BCC with macrophages in 2D and 3D. BCC did not show chemotaxis to macrophages in custom designed 3D cell-on-a-chip devices, which was in agreement with ELISA results showing that macrophage-derived-EGF was not secreted into macrophage-conditioned-medium. Live cell imaging of BCC in the presence and absence of iressa showed that macrophages but not macrophage-derivedmatrix modulated adhesion and motility of BCC in 2D. 3D co-culture experiments in matrigel and collagen showed that BCC changed their multicellular organization in the presence of macrophages. In custom designed 3D co-culture cell-on-a-chip devices, macrophages reduced and promoted migration of BCC in matrigel and collagen, respectively. Furthermore, adherent but not suspended BCC endocytosed EGFR when in contact with macrophages. Collectively, our data revealed that macrophages showed chemotaxis towards BCC-derived-CSF-1 whereas BCC required direct contact to interact with macrophage-derived-EGF. We propose that the interaction between cancer cells and macrophages is a paracrine-juxtacrine loop of CSF-1 and EGF, respectively.
Citation - WoS: 11
Citation - Scopus: 12
Novel Hybrid Process for the Conversion of Microcrystalline Cellulose To Value-Added Chemicals: Part 1: Process Optimization
(Springer Verlag, 2016-12) Akın, Okan; Yüksel, Aslı; 03.02. Department of Chemical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
In this paper, a novel hybrid process for the treatment of microcrystalline cellulose (MCC) under hot-compressed water was investigated by applying constant direct current on the reaction medium. Constant current range from 1A to 2A was applied through a cylindrical anode made of titanium to the reactor wall. Reactions were conducted using a specially designed batch reactor (450 mL) made of SUS 316 stainless steel for 30–120 min of reaction time at temperature range of 170–230 °C. As a proton donor H2SO4 was used at concentrations of 1–50 mM. Main hydrolysis products of MCC degradation in HCW were detected as glucose, fructose, levulinic acid, 5-HMF, and furfural. For the quantification of these products, High Performance Liquid Chromatography (HPLC) and Gas Chromatography with Mass Spectroscopy (GC–MS) were used. A ½ fractional factorial design with 2-level of four factors; reaction time, temperature, H2SO4 concentration and applied current with 3 center points were built and responses were statistically analyzed. Response surface methodology was used for process optimization and it was found that introduction of 1A current at 200 °C to the reaction medium increased Total Organic Carbon (TOC) and cellulose conversions to 62 and 81 %, respectively. Moreover, application of current diminished the necessary reaction temperature and time to obtain high TOC and cellulose conversion values and hence decreased the energy required for cellulose hydrolysis to value added chemicals. Applied current had diverse effect on levulinic acid concentration (29.9 %) in the liquid product (230 °C, 120 min., 2 A, 50 mM H2SO4). © 2016, Springer Science+Business Media Dordrecht.
Citation - WoS: 9
Citation - Scopus: 10
Novel Hybrid Process for the Conversion of Microcrystalline Cellulose To Value-Added Chemicals: Part 2: Effect of Constant Voltage on Product Selectivity
(Springer Verlag, 2017-11) Akın, Okan; Yüksel, Aslı; 03.02. Department of Chemical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
In this study, electrochemical degradation of microcrystalline cellulose (MCC) under hot-compressed water was investigated via application of constant voltage on reaction medium. Constant voltage ranges from 2.5 to 8.0 V was applied between anode (Titanium) and cathode (reactor wall). As an electrolyte and proton source 5–25 mM of H2SO4 was used. Reactions were carried out in a specially designed batch reactor (450 mL) made of T316 for 240 min at temperature of 200 °C.MCC decomposition products such as glucose, fructose, furfural, 5-HMF and levulinic acid were detected and quantified by High Performance Liquid Chromatography (HPLC). In the absence of electrolyte, applied voltage (2.5 and 4.0 V) decreased the total organic carbon (TOC) yield, in contrast at 8.0 V, TOC yield increased to 13%. Application of 8.0 V in hydrothermal conditions alter MCC decomposition pathway selectively to furfural (15%). Addition of electrolyte (5 mM, H2SO4) and application of 2.5 V potential increased TOC (54%) and changed the decomposition pathway in favor of 5-HMF (30%) and levulinic acid (21%). The structural changes in solid residues of electrochemically reacted MCC was analyzed by Fourier Transform Infrared Spectroscopy (FTIR) and found that MCC particles functionalized by carboxylic acid and sulfonated groups by the application of constant voltage to reaction medium. In the presence of electrolyte, under certain voltage (2.5 V), functionalization of solid particles became more obvious in FTIR spectrum results. Therefore, change in the selectivity values of degradation products were conducted with the functionalization of MCC particles due to applied voltage under sub-critical conditions.
Citation - WoS: 33
Citation - Scopus: 37
Steam Gasification of Safflower Seed Cake and Catalytic Tar Decomposition Over Ceria Modified Iron Oxide Catalysts
(Elsevier Ltd., 2014-10) Duman, Gözde; Watanabe, Taichi; Uddin, Md Azhar; Yanık, Jale; 01. Izmir Institute of Technology
Catalytic steam gasification of safflower seed cake was carried out using a double-bed microreactor in a two-stage process in the presence of ceria oxide (CeO2) modified iron oxide (Fe2O3) catalysts with different CeO2-Fe2O3 ratios. The effects of both catalyst and the temperature of catalytic bed on the tar decomposition and the overall gaseous product yield were investigated comparatively. It was found that ceria modified iron oxide catalysts had higher reactivity than that of the individual Fe2O3 and CeO2 for the catalytic tar decomposition in safflower seed cake steam gasification. The CeO2-Fe2O3 catalyst with 50 wt.% of Fe 2O3 exhibited the excellent performance for tar conversion at 700 °C. A comparison of tar decomposition from thermal run and catalytic run showed that in thermal run tar decomposition was progressed via steam reforming only. However, in the presence of catalyst, tar decomposition occurred via both steam reforming and water gas shift reaction. As a conclusion, ceria promoted iron catalysts were found to be active for both hydrogen production and tar decomposition in steam gasification of lignocellulosic biomass.
Citation - WoS: 19
Citation - Scopus: 22
Valorization of Hazelnut Shell Waste in Hot Compressed Water
(Elsevier Ltd., 2017) Gözaydın, Gökalp; Yüksel, Aslı; 03.02. Department of Chemical Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
Hydrothermal conversion of waste hazelnut shell in hot compressed water, green and environmentally friendly medium, was investigated under different operating conditions to clarify the effects of reaction temperature, reaction time, acid concentration and acid kind (H2SO4 and H3PO4) on the production of value-added chemicals with high temperature/high pressure autoclave. In literature, to our best knowledge, there is no study about the production of levulinic acid, as a high value chemical, from waste hazelnut shell in hot-compressed water without using any mineral and heterogeneous catalyst. Hydrothermal reactions were conducted at 150–280 °C for reaction times of 15 to 120 min with various H2SO4 and H3PO4 concentrations varying from 0 to 125 mM. The detailed liquid product species were identified with High Performance Liquid Chromatography (HPLC) and gaseous products were analyzed by Gas Chromatography with a Thermal Conductivity Detector (GC-TCD). The main identified liquid compounds were levulinic acid, acetic acid and furfural while carbon dioxide and carbon monoxide were the major gaseous products. Increasing the reaction temperature (280 °C) and reaction time (120 min) resulted in a significant increment on the conversion (65.40%) as well as levulinic acid yield (13.05%). The production of levulinic acid was enhanced with H2SO4 addition; whereas treatments with H3PO4 improved the furfural production.

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