TUBITAK Marmara Research Center
  • Marmara, Kocaeli, Turkey
Recent publications
In this study, Ta nanopillar array was prepared using Anodic aluminium oxide (AAO) nanotemplate assisted method. Ta nanopillars are approximately 80 nm in width and 150 nm in length. In electrochemical measurements, the electrons in the Ta nanopillars and ions in the H2SO4 electrolyte formed the electrical double layer supercapacitor (EDLC). The specific capacitance of the Ta nanopillar array electrode was 640 Fg⁻¹. Ta nanopillar array electrode has 86% retention after 1000 cycles. The results reveal that the Ta nanopillar array-based electrode is a potential candidate electrode material for supercapacitors.
As diabetes has become one of the major health problems affecting hundreds of millions of people worldwide, the development of electrochemical sensors for the detection of glucose is crucial. Herein, the fabrication of nickel phthalo-cyanine (NiPc)-based and NiPc-borophene nanocomposite-based non-enzy-matic electrochemical sensors for glucose detection at room temperature was demonstrated. The electrical conductivities of NiPc and NiPc-borophene nanocomposite have been measured as 3 9 10-13 S cm-1 and 9.5 9 10-9 S cm-1 , respectively. The electrical conductivity of NiPc has been improved with the addition of borophene. Due to the high charge transport advantages of the borophene additive, the sensor sensitivity and detection limit have been improved. In voltammetric cycle of 60 s for the 1.5-24 mM glucose concentration range, NiPc-based sensor has a sensitivity value of 0.08 lAmM-1 cm-2 , while the NiPc-borofen nanocomposite-based sensor has a much higher sensitivity of 10.31 lAmM-1 cm-2. The limit of detection values of the NiPc and NiPc-borophene nanocomposite-based sensors are 3 lM and 0.15 lM, respectively. The borophene nanosheets with good chemical stability and high carrier mobility have been shown to be a good candidate to form nanocomposite structure with NiPc for glucose detection.
The COVID-19 outbreak caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to have high incidence and mortality rate globally. To meet the increasingly growing demand for new therapeutic drugs and vaccines, researchers are developing different diagnostic techniques focused on screening new drugs in clinical use, developing an antibody targeting a SARS-CoV-2 receptor, or interrupting infection/replication mechanisms of SARS-CoV-2. Although many prestigious research publications are addressing this subject, there is no open access platform where all experimental techniques for COVID-19 research can be seen as a whole. Many researchers have accelerated the development of in silico methods, high-throughput screening techniques, and in vitro assays. This development has played an important role in the emergence of improved innovative strategies including different antiviral drug development, new drug discovery protocols, combinations of approved drugs, and setting up new drug classes during the COVID 19 outbreak. Hence, the present review discusses the current literature on these modalities, including virtual in silico methods for instant ligand- and target-driven based techniques, nucleic acid amplification tests, and in vitro models based on sensitive cell cultures, tissue equivalents, organoids, and SARS-CoV-2 neutralization systems (lentiviral pseudotype, viral isolates, etc.). This pack of complementary tests inform researchers about the accurate, and most relevant emerging techniques available, and in vitro assays allowing them to understand their strengths and limitations. This review could be a pioneer reference guide for the development of logical algorithmic approaches for new drugs and vaccine strategies against COVID-19.
In this study, a series of peripherally and non-peripherally tetra-substituted metal-free and zinc(II) phthalocyanines were successfully prepared in good yields by cyclotetramerization of the phthalonitrile derivative bearing a tetraethylene glycol methyl ether group at 3- and 4- positions. All newly synthesized compounds were characterized using spectroscopic methods, such as FT-IR, NMR, mass and UV-Vis spectroscopy. To determine the therapeutic potential of the synthesized phthalocyanines, the effects of the substitution pattern (peripheral and non-peripheral) and central metal atom on the photophysicochemical properties were investigated. When comparing their singlet oxygen generation capabilities (ΦΔ), metallo-phthalocyanine derivatives with zinc (0.73 for 1b and 0.70 for 2b) showed higher singlet oxygen yield than metal-free derivatives (0.21 for 1a and 0.12 for 2a) in DMSO. The photodynamic therapy activities of the water-soluble phthalocyanines were tested via in vitro studies using the A253, FaDu (head and neck cancer cell lines), and HT29 (colon cancer) cell lines. The strongest photodynamic activity was found in 1b and 2b molecules with a metal core among the four molecules studied. The results suggested that the non-peripherally tetra-substituted 1b molecule was regarded as a suitable photodynamic therapy agent due to its light cytotoxicity and secondary impact induced by ROS production.
In this study, ethanol detection performance of divanadium pentoxide (V2O5) nanowire array was investigated at various temperatures. The main purpose of this study is to develop a novel V2O5 nanowires-based sensor for the detection of ethanol using an Anodic Aluminum Oxide (AAO) template by direct voltage electrodeposition at room temperature. It was observed that the V2O5 nanowires were approximately 60 nm in diameter in a large area of 6 cm². X-ray Diffraction (XRD) spectrum indicated the formation of V2O5. The XRD peak was indexed as V2O5 located at 2θ°≅ 20° that is attributed to the (001) lattice plane. The sensitivity of the V2O5 nanowire array was found 0.24 at 200 °C for 50 ppm ethanol. The results reveal that the diffusivity of the V2O5 molecules increases rapidly with increasing temperature, causing an increased sensitivity. The maximum sensor response was obtained at 200 °C. The limit of detection (LOD) of the V2O5 nanowire array sensor was 500 ppb at 200 °C. The response time (t90) of the V2O5 nanowire array sensor was calculated to be 52 s and the recovery time was 26 s at 200 °C.
In the present study, polycyclic aromatic hydrocarbon (PAH) accumulation performances of four butyl rubber (BR) monophasic passive samplers with different pore structures were investigated and the results were compared with monophasic polydimethylsiloxane (PDMS) samplers and biphasic semipermeable membrane devices (SPMDs). Stainless steel cages containing passive samplers were deployed in the water column in Istinye Bay, Istanbul Strait, and retrieved after 7 and 28 days. Collected samplers were analyzed using high-performance liquid chromatography (HPLC) to determine their PAH contents. Results showed that BR passive samplers have sampled all PAHs for both short- and long-term sampling periods while SPMD samplers only collected twelve and thirteen PAHs after 7 and 28 days, respectively. PDMS samplers showed the poorest performance, having only sampled seven and ten PAHs after 7 and 28 days, respectively. Among the BR samplers, a monophasic BR sampler with a single pore network (SN10) showed the most feasible performance in terms of PAH sampling and its preparation cost. Results highlighted that the SN10 sampler with a wide absorption range and monophasic structure can be used as an alternative passive sampler for pollution monitoring in marine environments.
Carbon dioxide methanation process is a well-known carbon dioxide utilization technology, not only on account of its ability to subside carbon dioxide in the atmosphere but also to produce methane, which is of serious industrial significance. Although this process is promising in terms of tackling greenhouse gases and global warming, it can, on the other hand, release toxic emissions into the atmosphere, rivers and soil during the process. At this point, life cycle environmental assessment emerges as a crucial tool to reveal the overall effects of this technology. This paper presents a life cycle assessment case study for carbon dioxide methanation process to evaluate all aspects of its environmental impacts. Different scenarios for this purpose were considered by changing catalyst types, namely, mixed metal oxide and zeolite-supported metal catalysts. The results showed that the toxic wastes formed and emissions released when using the Ni/Al2O3 catalyst were less compared to the other cases. Not only did the change in material type in the catalyst affect the total emissions, but the catalyst conversion and selectivity had an influence on the life cycle impact of the system as well. Various power generation alternatives considering renewable and non-renewable sources were evaluated, while a combination of natural gas and wind turbines for the initial sources of power generation was found to perform better in terms of environmental impact.
Microcapsules containing probiotic culture mixture (Lactobacillus casei + Bifidobacterium longum) (1%), 1% sodium alginate, 2% fructooligosaccharide, 2% inulin were prepared. Symbiotic white cheese was obtained by adding free and microencapsulated probiotic bacteria and prebiotics to goat milk. The ripening biochemistry of the cheeses during 180 days of storage at +4°C was determined by some biochemical‐physical analysis methods, and the organic acid content of white goat cheese was determined. Dry matter, titration acidity, protein, total nitrogen, and organic acid values were higher in cheese samples containing microcapsules than the samples without capsules, while fat content, water‐soluble nitrogen, non‐protein nitrogen, and ripening coefficient values were lower (p<0.05). It has been determined that the ratio of lactic acid and pyruvic acid is high in cheese samples containing symbiotic microcapsules, while the amount of citric acid, acetic acid, and formic acid is high in cheeses containing probiotics and prebiotics in free form. It was concluded that the addition of symbiotic microcapsules in the production of white goat cheeses increased the quality criteria of the cheese.
In this study, open-type refrigeration cabinets were designed and manufactured using hot gas and electrical resistance defrost methods and R290, R449A and R404A refrigerants. The aim of this study is to determine the temperature increase of the products during the process, CO2 emission amount, defrost efficiency, and energy efficiency index (EEI) value with different defrost methods and refrigerants for commercial refrigeration systems. The increase in package temperatures during the defrosting process was determined as 1.33 °C in the electrical method. The results showed that the hot gas method was 7.15% more efficient in terms of defrosting efficiency. The EEI value was calculated as 78.76 with the use of R290 in the hot gas method and the energy class was determined as F and the hot gas emit 5.9% less CO2 than in the resistance experiments. In the hot gas defrost method, it was seen that 20.3% less energy was consumed compared to the total consumption. It was observed that R290 refrigerant and the hot gas defrost method were the most suitable for commercial systems in terms of defrosting process losses, total energy consumption, and temperature rise of the cooled product during defrosting.
Medicinal herbs and their essential oils are used in human health promotion and disease prevention since ancient times. In the last two decades, many studies have been carried out to both identify bioactive compounds in medicinal herbs and derived essential oils and to examine their biological effects in experimental models; clinical trials, however, have been scant. This review discusses in vitro, in vivo, and clinical evidence supporting the immunomodulatory role of eleven medicinal herbs (bay laurel, black cumin, clove, fennel, lemon balm, lemongrass, marjoram, peppermint, rosemary, sage, and thyme) and their essential oils and bioactive components. Safety and toxicity aspects for consumption as well as future perspectives are also covered. Relevant data from the existing literature have been compiled and summarized. These herbs and oils, which are increasingly consumed, can be considered as valuable dietary supplements due to their health-promoting bioactive constituents. Well-design clinical trials are warranted to better ascertain the immunomodulatory effects of these herbal products.
In this study, hybrid fiber mat (HFPP-CS) consisting of both chlorinated polypropylene and chitosan fibers (FPP-Cl and FCS) is obtained by assembling layer-by-layer for the first time using electrospinning process. Morphological, wettability, structural and thermal properties of HFPP-CS are investigated in detail by Scanning electron microscopy (SEM), water contact angle (WCA) measurement, fourier transform infrared spectroscopy, thermogravimetric analysis and differential scanning calorimetry analyses, respectively, comparing with FPP-Cl and FCS. Furthermore, the antibacterial activity of all samples was evaluated against to gram positive Staphylococcus aureus (S. aureus) and gram negative Escherichia coli (E. coli) bacteria. SEM analysis proves to HFPP-CS has a circular and smooth morphology and also comprises of microscale FPP-Cl and nanoscale FCS layers within the range of 2.1–2.7 μm and 175–475 nm, respectively. The incorporation of nano-FCS layer on micro-FPP-Cl layer leads to diminution in the hydrophobicity from WCA value of 137° ± 2 to 124° ± 2, but enhancement in the thermostability and glass transition temperature of the resulting fiber mat. The antibacterial activity results show that HFPP-CS has higher inhibition effect against to S. aureus and E. coli than FPP-Cl but lower than FCS. In general, it is anticipated that the prepared amphiphilic and antibacterial HFPP-CS can be employed as potential biomaterial for a variety of bioengineering applications. Graphical Abstract The novel hybrid fiber mat having natural and synthetic polymer layers has prepared by assembling layer-by-layer using electrospinning. The achieved amphiphilic hybrid fiber mat demonstrates higher thermal properties than that of each pristine fiber layer. The hybrid fiber mat has good antibacterial activity against to both gram positive and gram negative bacteria.
Hazardous substances used and produced by different industrial activities pose a potential risk to the environment and to human health. Different physicochemical and/or biological processes are used in industrial wastewater treatment; these methods, however, may not be effective in removing these substances. This study was carried out to comparatively evaluate the removal of hazardous substances through conventional wastewater treatment processes that are used by major industries in Turkey. A four-season monitoring study was carried out in textile manufacturing and leather production sectors, representing industrial activities in Turkey. Samples were analyzed for 45 priority substances defined by the European Union and 250 specific pollutants listed in the Turkish Regulation on Surface Water Quality. For both wastewaters, where biological treatment was performed after pretreatment, their characteristics showed that organics were almost completely removed. except for dichloromethane (44–51% removals) and dioxin and dioxin-like compounds (64–69% removals). Additionally, different removal ratios (16–97%) were obtained for metals; the poorer removal was observed for B, Ba, Ag, Sb, and Si. The remaining metals (Cu, Pb, Sb, V, Si for textile; Cr, Cu, Sb, Si for leather effluents) in the treated wastewaters were still higher than environmental quality standards (EQS) of receiving water bodies. The study revealed that existing treatment processes were not adequate for efficient hazardous substance removal and there is an urgent need to improve them. Finally, advanced treatment technologies were suggested for specific pollutants together with their unit treatment costs.
The aim of this study was to valorize Thymus serpyllum L. herbal dust, the particular fraction distinguished as industrial waste from filter-tea production. This work demonstrated comparable analysis considering model fitting, influence analysis and optimization of microwave-assisted extraction (MAE) of bioactive compounds from the aforementioned herbal dust using face-centered central composite experimental design within the response surface methodology (RSM), as well as artificial neural networks (ANN). In order to increase yield and amount of compounds of interest and minimize solvent, time and energy consumption, the ethanol concentration (45, 60 and 75%), extraction time (5, 12.5 and 20 min), liquid–solid ratio (10, 20 and 30 mL/g) and irradiation power (400, 600 and 800 W) were used as independent variables. Total extraction yield (Y), total phenols yield (TP), as well as antioxidant activity parameters obtained by DPPH and ABTS assays, were selected as responses. It could be concluded that the MAE technique is an efficient approach for the extraction of biologically active compounds from T. serpyllum herbal dust, which represents a high-value source of natural antioxidants with great potential for further use in various forms within different branches of industry.
Purpose MALT1 deficiency is a combined immune deficiency characterized by recurrent infections, eczema, chronic diarrhea, and failure to thrive. Clinical and immunological characterizations of the disease have not been previously reported in large cohorts. We sought to determine the clinical, immunological, genetic features, and the natural history of MALT-1 deficiency. Methods The clinical findings and treatment outcomes were evaluated in nine new MALT1-deficient patients. Peripheral lymphocyte subset analyses, cytokine secretion, and proliferation assays were performed. We also analyzed ten previously reported patients to comprehensively evaluate genotype/phenotype correlation. Results The mean age of patients and disease onset were 33 ± 17 and 1.6 ± 0.7 months, respectively. The main clinical findings of the disease were recurrent infections (100%), skin involvement (100%), failure to thrive (100%), oral lesions (67%), chronic diarrhea (56%), and autoimmunity (44%). Eosinophilia and high IgE were observed in six (67%) and two (22%) patients, respectively. The majority of patients had normal T and NK cells, while eight (89%) exhibited reduced B cells. Immunoglobulin replacement and antibiotics prophylaxis were mostly ineffective in reducing the frequency of infections and other complications. One patient received hematopoietic stem cell transplantation (HSCT) and five patients died as a complication of life-threatening infections. Analyzing this cohort with reported patients revealed overall survival in 58% (11/19), which was higher in patients who underwent HSCT (P = 0.03). Conclusion This cohort provides the largest analysis for clinical and immunological features of MALT1 deficiency. HSCT should be offered as a curative therapeutic option for all patients at the early stage of life.
We have designed and synthesized a pair of highly asymmetric D-aA-D’ type pyridyl-sulfonyl based isomers comprising phenothiazine (PTZ) and carbazole (Cz) donor units, which are able to emit thermally activated delayed fluorescence. PTZ-pS4-Py-2Cz and PTZ-mS4-Py-2Cz both possess spatial separation of HOMO/LUMO on the donor and acceptor moieties, resulting in small calculated singlet–triplet energy gaps (~0.25 eV). Both isomers exhibit dual emission, which is attributed to charge transfer states associated with the Cz and PTZ moieties at higher and lower energies, respectively. Photoluminescence quantum yields and time-resolved emission decays show significant differences for the two isomers, with the para- isomer exhibiting more efficient emission and stronger delayed fluorescence than the meta- isomer – in strong contrast to recently reported analogous Cz-Cz D-aA-D isomers. The findings clearly show that the interconversion of triplets via the rISC mechanism is promoted when parallel Cz and PTZ charge transfer states are allowed to interact, explaining the improved performance of the Cz-PTZ materials compared to the previous Cz-Cz ones. Finally, moderate device performance was achieved in warm-yellowish (CIE; 0.41; 0.53 & 0.49; 0.48) non-doped OLEDs, which exhibited 0.5% & 1.9% maximum external quantum efficiencies for the meta- and para- isomers, respectively.
Poly(2‐oxazoline)s are a class of organic polymers having tertiary amide groups in their chemical structure. They are currently under intense study for potential applications in many different fields due to the tunability of their physical and chemical properties. In this work, poly(2‐oxazoline)s are demonstrated for the first time as the sensing elements for chemical sensors. More specifically, a poly(2‐n‐propyl‐2‐oxazoline) (PnPropOx) with a xanthate end‐group is synthesized and used to modify a quartz crystal microbalance (QCM) transducer. The general liquid sensing properties and sensor responses of the resulting PnPropOx‐QCM sensor to a variety of ionic compounds in aqueous solutions have been evaluated revealing excellent liquid sensing properties showing a strong response to alkali chlorides and cyanides, especially. The sensor response is fast and fully reversible and the selectivity for alkali chlorides and cyanides is remarkably high. The observed sensitivity using 5 MHz PnPropOx‐QCMs reaches ≈8 Hz µM−1 at 30 °C, enabling analyte detection down to a limit of detection of 0.2 µM concentration. According to these results, it can be concluded that PnPropOx, and possibly poly(2‐oxazoline)s in general, is very promising as a sensing material for chemical sensors in liquids to selectively detect a variety of ionic species. Poly(2‐n‐propyl‐2‐oxazoline) has been applied as the sensing element in a chemical quartz crystal microbalance sensor revealing sensing responses to a variety of salts in an aqueous solution. The resulting sensor is found to have fast and reversible sensing properties showing strong responses to alkali chlorides and cyanides with sensitivity down to concentrations ≈0.2 µM.
In this study, the phenolic compounds of oil mill waste (OMW) were extracted through cloud point extraction method using lecithin as a surfactant. For this purpose, the effects of the equilibration temperature and time, pH and the concentration of NaCl and lecithin on the recovery (%) of total phenolic content (TPC) were investigated to by single factor experiments and further optimization of the process variables was carried out by using the response surface analysis. The TPC values of OMW were 4830.50 ± 414.7 mg GAE/L, 7545.25±766.89 TyE/L and 5220.22 ± 390.68. HyTE/L. Antioxidant capacity values were 6892.05±222.64 mg TE/L, 5010.54±216.90 mg Fe2+E / L and 4315.06 ± 237.73 mg TE/L. The hydroxytyrosol was the main phenolic compound identified with the value of 592.91±8.39 mg/L followed by tyrosol at the level of 167.34±2.23 mg/L. The optimum process conditions were determined as the temperature of 650C, pH of 4.5, NaCl concentration of 10% (w:v) and the lecithin concentration of 15% (w:v). The enriched lecithin obtained under the optimum conditions was used in the formulation of salad dressing, and its oxidative stability was compared to the sample prepared by control lecithin. The oxidation kinetic parameters namely, IP, Ea, ΔH++∆S++, and ∆G++ showed that the salad dressings prepared with enriched lecithin provided higher oxidative stability than control lecithin. This study suggested that the use of lecithin in cloud point extraction could offer a new perspective for the recovery of phenolics from OMW without the application of solvent.
Textile industry is one of the major water-consuming sectors; therefore, developing methods for reusing water is essential. Processes including reverse osmosis (RO) have gained momentum recently and been widely used. However, concentrated streams (brine) generated from RO must be managed properly. In this study, a pilot-scale brine treatment system containing ozone oxidation, nanofiltration (NF), RO and ion exchange (IEX) was developed and operated to recover a high quality process water and salt solution to be reused in dyeing processes. It was revealed that 77% of the water and 66% of the salt solution (as NaCl) can be recovered and brine discharge can be reduced. With full-scale operation for one year, it is possible to achieve cost-savings by 176,256 USD with 115,000 m³ reused water and by 37,000 USD with 680 tons of recovered NaCl. Recovery of brine makes it possible to achieve sustainable production and zero liquid discharge concepts.
Climate observations inform about the past and present state of the climate system. They underpin climate science, feed into policies for adaptation and mitigation, and increase awareness of the impacts of climate change. The Global Climate Observing System (GCOS), a body of the World Meteorological Organization (WMO) assesses the maturity of the required observing system and gives guidance for its development. The Essential Climate Variables (ECVs) are central to GCOS and the global community must monitor them with the highest standards in the form of Climate Data Records (CDR). Today, a single ECV - the sea ice ECV - encapsulates all aspects of the sea-ice environment. In the early 1990s it was a single variable (sea-ice concentration) but is today an umbrella for four variables (adding thickness, edge/extent, and drift). In this contribution, we argue that GCOS should from now on consider a set of seven ECVs (sea-ice concentration, thickness, snow-depth, surface temperature, surface albedo, age, and drift). These seven ECVs are critical and cost-effective to monitor with existing satellite Earth Observation capability. We advise against placing these new variables under the umbrella of the single sea ice ECV. To start a set of distinct ECVs is indeed critical to avoid adding to the sub-optimal situation we experience today, and to reconcile the sea ice variables with the practice in other ECV domains. This work was presented at the 29 th GCOS Steering Committee meeting in December 2021.
Background Obesity is a complex genetic-based pediatric disorder which triggers life-threatening conditions. Therefore, the understanding the molecular mechanisms of obesity has been a significant approach in medicine. Computational methods allow rapid and comprehensive pathway analysis, which is important for generation of diagnosis and treatment of obesity.Methods and resultsAims of our study are to comprehensively investigate genetic characteristics of obesity in children with non-syndromic, early-onset (< 7 years), and severe obesity (BMI-SDS > 3) through computational approaches. First, the mutational analyses of 41 of obesity-related genes in 126 children with non-syndromic early-onset severe obesity and 76 healthy non-obese controls were performed using the next generation sequencing (NGS) technique, and the NGS data analyzed by using bioinformatics methods. Then, the relationship between pathogenic variants and anthropometric/biochemical parameters was further evaluated. Obtained results demonstrated that the 15 genes (ADIPOQ, ADRB2, ADRB3, IRS1, LEPR, NPY, POMC, PPARG, PPARGC1A, PPARGC1B, PTPN1, SLC22A1, SLC2A4, SREBF1 and UCP1) which directly related to obesity found linked together via biological pathways and/or functions. Among these genes, IRS1, PPARGC1A, and SLC2A4 stand out as the most central ones. Furthermore, 12 of non-synonymous pathogenic variants, including six novels, were detected on ADIPOQ (G90S and D242G), ADRB2 (V87M), PPARGC1A (E680G, A477T, and R656H), UCP1 (Q44R), and IRS1 (R302Q, R301H, R301C, H250P, and H250N) genes.Conclusion We propose that 12 of non-synonymous pathogenic variations detected on ADIPOQ, ADRB2, PPARGC1A, UCP1, and IRS1 genes might have a cumulative effect on the development and progression of obesity.
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290 members
Ozgur Duygulu
  • Materials Institute
Esin Aslankaraoglu Akcael
  • Genetic Engineering and Biotechnology Institute
Saban Tekin
  • Genetic Engineering and Biotechnology Institute
Leyla Tolun
  • Environment Institute
41470, Marmara, Kocaeli, Turkey