174 results on '"Kanik A"'
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2. Usage of Barium Titanate in Fabric Coating and Investigation of Some Properties
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Rumeysa Celen, Gizem Manasoglu, Mehmet Kanik, and Yusuf Ulcay
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Tear resistance ,Materials science ,Polymers and Plastics ,Scanning electron microscope ,General Chemical Engineering ,02 engineering and technology ,General Chemistry ,engineering.material ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Coating ,Air permeability specific surface ,Electromagnetic shielding ,Barium titanate ,Transmittance ,engineering ,Fourier transform infrared spectroscopy ,Composite material ,0210 nano-technology - Abstract
In this study, nano-sized barium titanate powder was applied for the first time to polyester woven fabrics by knife coating at three different concentration rates. Some physical (thickness, mass per unit area, bending rigidity, air permeability and tear strength) properties, electromagnetic shielding efficiency and solar (transmittance, reflectance) properties of samples were presented. The samples were also characterized by Fourier transform infrared spectroscopy and scanning electron microscopy. Electromagnetic shielding effectiveness of the fabrics was determined according to the ASTM D4935-10 standard by using a coaxial transmission line measurement technique in the frequency range of 15–3000 MHz. The solar properties were measured according to EN14500 standard using a UV/VIS/NIR spectrophotometer and results were calculated according to EN 410 standard. Results revealed that the electromagnetic shielding effectiveness and solar reflectance property of samples improved with increasing barium titanate concentration.
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- 2021
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3. Bazı bitki ektraktlarının Sitophilus granarius (Linnaeus, 1758) (Coleoptera: Curculionidae) ve Tribolium castaneum (Herbst, 1797) (Coleoptera: Tenebrionidae) üzerindeki insektisidal ve davranışsal etkileri
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Ömer Cem Karakoç and Feride Kanik
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Apiaceae ,biology ,Achillea ,Sitophilus ,Ethyl acetate ,biology.organism_classification ,Salvia wiedemannii ,chemistry.chemical_compound ,Horticulture ,chemistry ,Curculionidae ,General Earth and Planetary Sciences ,Lamiaceae ,Red flour beetle ,General Environmental Science - Abstract
Depolanmış ürünlerdeki böceklerle mücadele oldukça önemlidir. Sitophilus granarius (Linnaeus, 1758) (Coleoptera: Curculionidae) ve Tribolium castaneum (Herbst, 1797) (Coleoptera: Tenebrionidea) depolanmış ürünlerde zarar meydana getiren önemli iki zararlı böcek türüdür. Depolanmış ürünlerdeki zararlılarla mücadelede kullanılabilecek alternatif ilaçlara ise her geçen gün ihtiyaç artmaktadır. Bu çalışmada, Achillea phrygia Boiss. et Bal. (Compositae), Prangos ferulacea (L.) Lindl. (Apiaceae) ve Salvia wiedemannii Boiss. (Lamiaceae) bitkilerinden elde edilen bitki ekstraktlarının, S. granarius ve T. castaneum ile mücadelede kullanılabilirlikleri araştırılmıştır. 72 saat sonunda, S. garanarius üzerinde test edilen bitkiler arasında en yüksek kontak aktiviteyi sırasıyla %74 ile P. ferulaceae hekzan, %71 ile A. phrygia methanol ekstraktı göstermiştir. T. castaneum üzerinde en yüksek aktiviteyi ise 72 saat sonunda %42 ile A. phrygia etil asetat ekstraktı göstermiştir. Bitki ekstraktları ile yapılan davranışsal etki çalışmalarında ise S. granarius üzerindeki en yüksek repellent aktivite 24. saat sonunda P. ferulaceae etil asetat ekstraktından (%52) elde edilmiştir. Bitki ekstraktlarının tamamı T. castaneum üzerinde yüksek oranda repellent etki göstermiştir.
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- 2020
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4. Selectively Micro-Patternable Fibers via In-Fiber Photolithography
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Yoel Fink, Polina Anikeeva, Mehmet Kanik, Andres Canales, Youngbin Lee, and Gabriel Loke
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Materials science ,010405 organic chemistry ,business.industry ,General Chemical Engineering ,General Chemistry ,Photoresist ,010402 general chemistry ,01 natural sciences ,Symmetry (physics) ,0104 chemical sciences ,law.invention ,Chemistry ,Photopolymer ,Semiconductor ,law ,Thermal ,Optoelectronics ,Fiber ,Photolithography ,business ,Axial symmetry ,QD1-999 ,Research Article - Abstract
Multimaterial fibers engineered to integrate glasses, metals, semiconductors, and composites found applications in ubiquitous sensing, biomedicine, and robotics. The longitudinal symmetry typical of fibers, however, limits the density of functional interfaces with fiber-based devices. Here, thermal drawing and photolithography are combined to produce a scalable method for deterministically breaking axial symmetry within multimaterial fibers. Our approach harnesses a two-step polymerization in thiol–epoxy and thiol–ene photopolymer networks to create a photoresist compatible with high-throughput thermal drawing in atmospheric conditions. This, in turn, delivers meters of fiber that can be patterned along the length increasing the density of functional points. This approach may advance applications of fiber-based devices in distributed sensors, large area optoelectronic devices, and smart textiles., Thermally drawable photoresist based on thiol−epoxy/thiol−ene network enables high-throughput fabrication of hundreds of meters of longitudinally patternable multimaterial fibers.
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- 2020
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5. Simulating Serpentinization as It Could Apply to the Emergence of Life Using the JPL Hydrothermal Reactor
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Galen D. Stucky, Takazo Shibuya, Rohit Bhartia, Lance E. Christensen, Isik Kanik, Lauren M. White, Adam Hoffmann, Michael J. Russell, Richard D. Kidd, and Steven D. Vance
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010504 meteorology & atmospheric sciences ,Earth, Planet ,Oceans and Seas ,Hadean ,Origin of Life ,Magnesium Compounds ,01 natural sciences ,Methane ,Hydrothermal circulation ,Astrobiology ,chemistry.chemical_compound ,Hydrothermal Vents ,Acetyl Coenzyme A ,0103 physical sciences ,Seawater ,Formate ,010303 astronomy & astrophysics ,0105 earth and related environmental sciences ,Silicates ,fungi ,Carbon Dioxide ,Agricultural and Biological Sciences (miscellaneous) ,chemistry ,Space and Planetary Science ,Iron Compounds ,geographic locations ,Hydrogen - Abstract
The molecules feeding life's emergence are thought to have been provided through the hydrothermal interactions of convecting carbonic ocean waters with minerals comprising the early Hadean oceanic crust. Few laboratory experiments have simulated ancient hydrothermal conditions to test this conjecture. We used the JPL hydrothermal flow reactor to investigate CO
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- 2020
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6. Role of interface layer in improving the efficiency of thin film silicon solar cell
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Rajib Chakraborty, Kanik Palodhi, Soumen Maiti, and Arnab Panda
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Materials science ,Silicon ,business.industry ,Cost effectiveness ,Band gap ,Energy conversion efficiency ,chemistry.chemical_element ,Atomic and Molecular Physics, and Optics ,Electronic, Optical and Magnetic Materials ,Gallium arsenide ,chemistry.chemical_compound ,chemistry ,Optoelectronics ,Crystalline silicon ,Electrical and Electronic Engineering ,Thin film ,business ,Layer (electronics) - Abstract
Lower photonic conversion efficiency along with complexity of fabrication are the primary constrains for cost effective thin film solar cell production. In this work, a planar single junction structure of thin film solar cell made with two different active materials is studied, which can take care of the mentioned problems. The active materials were selected based on different parameters like band gap energy, contact potential, lattice mismatch and cost effectiveness. Simulation shows that optical absorption along with photonic conversion efficiency varies due to change in position, thickness and doping concentration of active material and so these parameters are optimized accordingly. Here an interface layer of Gallium Arsenide (GaAs) is added to the thin film Silicon (Si) layer. Our optimized Si-GaAs based thin film solar cell yields a short circuit current density of 27.51 mA/cm2 with conversion efficiency of 13.71% having a fill factor of 0.81 under AM1.5G for a typical thin film solar cell of total thickness 2 µm out of which 80% is crystalline Silicon (1.6 µm thick) and 20% is Gallium arsenide (0.4 µm thick). Thus, a simple structure with improved conversion efficiency is proposed.
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- 2021
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7. Erythrocyte Membrane Protein Band 3 Predicts Interferon Ribavirin-Induced Anemia
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Serap Yalin, Anil Tombak, Engin Altintaş, Arzu Kanik, Enver Üçbilek, and Orhan Sezgin
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chemistry.chemical_classification ,medicine.medical_specialty ,Anemia ,business.industry ,Ribavirin ,medicine.disease ,Gastroenterology ,Erythrocyte Membrane Protein Band 3 ,chemistry.chemical_compound ,chemistry ,Interferon ,Internal medicine ,medicine ,Ankyrin ,Spectrin ,In patient ,business ,Polyacrylamide gel electrophoresis ,medicine.drug - Abstract
Aim & Background: It was proposed that the differences in erythrocyte membrane protein contents—especially band 4—take a role in the serious anemia related to interferon plus ribavirin (I/R). The aim of this study is to evaluate whether the erythrocyte membrane protein contents predict anemia related to I/R or not. Methods: 180 mcg interferon α 2a once a week and weight adjusted ribavirin daily were given for 48 weeks to fifty patients with chronic hepatitis C. It was diagnosed as anemia when haemoglobin concentration was
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- 2019
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8. Anti-VEGF treatment suppresses remodeling factors and restores epithelial barrier function through the E-cadherin/β-catenin signaling axis in experimental asthma models
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Ozge Yilmaz, Ahmet Türkeli, Sevinc Inan, Fatih Firinci, Meral Karaman, Esra Toprak Kanik, and Hasan Yuksel
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0301 basic medicine ,Cancer Research ,medicine.medical_specialty ,Platelet-derived growth factor ,medicine.medical_treatment ,Fibroblast growth factor ,adherens junction ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Immunology and Microbiology (miscellaneous) ,Epidermal growth factor ,Internal medicine ,medicine ,FGF ,EGF ,remodeling ,biology ,business.industry ,Growth factor ,E-cadherin ,PFGF ,General Medicine ,Articles ,anti-TNF ,β-catenin ,Vascular endothelial growth factor ,030104 developmental biology ,Endocrinology ,chemistry ,030220 oncology & carcinogenesis ,biology.protein ,Tumor necrosis factor alpha ,business ,Platelet-derived growth factor receptor ,Transforming growth factor - Abstract
Besides maintaining a physical barrier with adherens junctional (AJ) and tight junctional proteins, airway epithelial cells have important roles in modulating the inflammatory processes of allergic asthma. E-cadherin and beta-catenin are the key AJ proteins that are involved in airway remodeling. Various mediators such as transforming growth factor-beta (TGF-beta), epidermal growth factor (EGF), fibroblast growth factor (FGF), platelet derived growth factor (PDGF), insulin-like growth factor (IGF), tumor necrosis factor-alpha (TNF-alpha) and angiogenic factors, such as vascular endothelial growth factor (VEGF), are released by the airway epithelium in allergic asthma. The signaling pathways activated by these growth factors trigger epithelial-mesenchymal transition (EMT), which contributes to fibrosis and subsequent downregulation of E-cadherin. The present study used a mouse asthma model to investigate the effects of anti-VEGF, anti-TNF and corticosteroid therapies on growth factor and E-cadherin/beta-catenin expression. The study used 38 male BALB/c mice, divided into 5 groups. A chronic mouse asthma model was created by treating 4 of the groups with inhaled and intraperitoneal ovalbumin (n= 8 per group). Saline, anti-TNF-alpha (etanercept), anti-VEGF (bevacizumab) or a corticosteroid (dexamethasone) were applied to each group by intraperitoneal injection. No medication was administered to the control group (n=6). Immunohistochemistry for E-cadherin, beta-catenin and growth factors was performed on lung tissues and protein expression levels assessed using H-scores. Statistically significant differences were observed in E-cadherin, beta-catenin, EGF, FG, and PFGF (P0.005). All treatment groups had reduced TGF-beta, PDGF and FGF H-scores in comparison with the untreated asthma group (P=0.001). The EGF and IGF levels were not significantly different between the untreated asthmatic and non-asthmatic controls. The results suggested that anti-VEGF and TNF-alpha inhibition treatments are effective in decreasing growth factors, in a similar manner to conventional corticosteroid treatments. Anti-VEGF and TNF inhibition therapy may be an effective treatment for remodeling in asthma while offering an alternative therapeutic option to steroid protective agents. The data suggested that anti-VEGF treatment offered greater restoration of the epithelial barrier than both anti-TNF-alpha and corticosteroid treatment.
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- 2021
9. Structural characterization of unsaturated phosphatidylcholines using traveling wave ion mobility spectrometry
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Kim, Hugh I., Kim, Hyungjun, Pang, Eric S., Ryu, Ernest K., Beegle, Luther W., Loo, Joseph A., Goddard, William A., and Kanik, Isik
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Spectrum analysis -- Usage ,Lecithin -- Structure ,Lecithin -- Chemical properties ,Molecular dynamics -- Research ,Ionic mobility -- Analysis ,Chemistry - Abstract
A number of phosphatidylcholine (PC) cations spanning a mass range of 400-1000 Da are investigated using electrospray ionization mass spectrometry coupled with traveling wave ion mobility spectrometry (TWIMS). A high correlation between mass and mobility is demonstrated with saturated phosphatidylcholine cations in [N.sub.2]. A significant deviation from this mass--mobility correlation line is observed for the unsaturated PC cation. We found that the double bond in the acyl chain causes a 5% reduction in drift time. The drift time is reduced at a rate of ~1% for each additional double bond. Theoretical collision cross sections of PC cations exhibit good agreement with experimentally evaluated values. Collision cross sections are determined using the recently derived relationship between mobility and drift time in TWIMS stacked ring ion guide (SRIG) and compared to estimated collision cross sections using an empiric calibration method. Computational analysis was performed using the modified trajectory (TJ) method with nonspherical [N.sub.2] molecules as the drift gas. The difference between estimated collision cross sections and theoretical collision cross sections of PC cations is related to the sensitivity of the PC cation collision cross sections to the details of the ion--neutral interactions. The origin of the observed correlation and deviation between mass and mobility of PC cations is discussed in terms of the structural rigidity of these molecules using molecular dynamic simulations. 10.1021/ac900672a
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- 2009
10. Experimental and theoretical investigation into the correlation between mass and ion mobility for choline and other ammonium cations in [N.sub.2]
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Kim, Hyungjun, Kim, Hugh I., Johnson, Paul V., Beegle, Luther W., Beauchamp, J.L., Goddard, William A., and Kanik, Isik
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Mass (Physics) -- Research ,Ionic mobility -- Research ,Choline -- Chemical properties ,Cations -- Chemical properties ,Chemistry - Abstract
A number of tertiary amine and quaternary ammonium cations spanning a mass range of 60-146 amu (trimethylamine, tetramethylammonium, trimethylethylammonium, N,N-dimethylaminoethanoi, choline, N, N-dimethylglycine, betaine, acetylcholine, (3-carboxypropyl)trimethylammonium) were investgated using electrospray ionization ion mobility spectrometry. Measured ion mobilities demonstrate a high correlation between mass and mobility in [N.sub.2]. In addition, identical mobilities within experimental uncertainties are observed for structurally dissimilar ions with similar ion masses. For example, dimethylethylammonium (88 amu) cations and protonated N, N-dimethylaminoethanol cations (90 amu) show identical mobilities (1.93 [cm.sup.2] [V.sup.-1] [s.sup.-1]) though N,Ndimethylaminoethanol contains a hydroxyl functional group while dimethylethylammonium only contains alkyl groups. Computational analysis was performed using the modified trajectory (TJ) method with nonspherical [N.sub.2] molecules as the drift gas. The sensitivity of the ammonium cation collision cross sections to the details of the ion-neutral interactions was investigated and compared to other classes of organic molecules (carboxylic acids and abiotic amino acids). The specific charge distribution of the molecular ions in the investigated mass range has an insignificant affect on the collision cross section.
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- 2008
11. Characteristics of Children with Coronavirus Disease-2019 From The Pediatric Emergency Room
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Ali Kanik, Emel Berksoy, Gülşah Demir, Pelin Elibol, Dilek Yılmaz Çiftdoğan, Alper Çiçek, Gamze Gökalp, Şefika Bardak, Tuğçe Çelik, and Nisel Yilmaz
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medicine.medical_specialty ,business.industry ,Lymphocyte ,medicine.disease_cause ,medicine.disease ,Virus ,chemistry.chemical_compound ,Pneumonia ,medicine.anatomical_structure ,chemistry ,Lactate dehydrogenase ,Internal medicine ,Epidemiology ,medicine ,Coinfection ,Rhinovirus ,Respiratory system ,business - Abstract
We describe the demographic, clinical, and laboratory characteristics of children with COVID 19 in comparison with those of not-laboratory-confirmed cases. We conducted a cross-sectional study on the epidemiological, clinical, radiological, and laboratory characteristics, and outcome of 422 children (aged 0–18 years) with suspected and confirmed COVID 19 admitted to the pediatric emergency department from March 23rd to July 23rd, 2020. Of the 422 children with suspected COVID-19 included in this study, COVID-19 was PCR-confirmed in 78 (18.4%). Fever (51.2%) and cough (43.5%) were the most prominent symptoms in children with confirmed cases. The clinical status of the patients with confirmed COVID-19 was significantly milder than that of those with suspected COVID-19. The proportion of COVID-19 pneumonia cases was 44.4%, 5.5%, 18.7%, and 8.5% for the age groups of ≤ 1, 2–6, 7–12, and ≥ 12 years, respectively. Of the 422 children, 128 (30.3%) underwent nasopharyngeal PCR testing for other respiratory viral pathogens; 21 (16.4%) were infected with viral pathogens other than severe acute respiratory syndrome-related coronavirus-2. Only one patient (4.7%) with confirmed COVID-19 had coinfection with respiratory syncytial virus and rhinovirus. The areas under the receiver-operating characteristics curves were 0.812 for WBCs, 0.752 for neutrophils, 0.717 for lactate dehydrogenase, and 0.708 for lymphocyte for predicting COVID-19 (p ≤ 0.001). Fever and cough or other clinical symptoms or signs should not be considered hallmarks of COVID 19. In this study, the WBC, neutrophil, and lymphocyte counts were predictive of COVID-19 positivity.
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- 2020
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12. Highly Multiplexed Label-Free Imaging Sensor for Accurate Quantification of Small-Molecule Binding Kinetics
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John J Rejman, Matthew T. Geib, Elisa Chiodi, M. Selim Ünlü, Allison M. Marn, Fulya Ekiz Kanik, and David Ankrapp
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Chemistry ,General Chemical Engineering ,Kinetics ,General Chemistry ,Small molecule ,Multiplexing ,Receptor–ligand kinetics ,Article ,Drug development ,Biophysics ,Small molecule binding ,Image sensor ,QD1-999 ,Label free - Abstract
Investigating the binding interaction of small molecules to large ligands is a compelling task for the field of drug development, as well as agro-biotechnology, since a common trait of drugs and toxins is often a low molecular weight (MW). Here, we improve the limit of detection of the Interferometric Reflectance Imaging Sensor (IRIS), a label-free, highly multiplexed biosensor, to perform small-molecule screening. In this work, characterization of small molecules binding to immobilized probes in a microarray format is demonstrated, with a limit of detection of 1 pg/mm2 in mass density. First, as a proof of concept to show the impact of spatial and temporal averaging on the system noise, detection of biotin (MW = 244.3 Da) binding to a streptavidin-functionalized chip is performed and the parameters are tuned to achieve maximum signal-to-noise ratio (SNR ≈ 34). The optimized system is then applied to the screening of a 20-multiplexed antibody chip against fumonisin B1 (MW = 721.8 Da), a mycotoxin found in cereal grains. The simultaneously recorded binding curves yield an SNR ≈ 8. Five out of twenty antibodies are also screened against the toxin in a lateral flow assay, obtaining consistent results. With the demonstrated noise characteristics, further sensitivity improvements are expected with the advancement of camera sensor technology.
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- 2020
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13. Effect of modified double-sided grating structures on efficiency enhancement of thin-film silicon solar cells
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Kanik Palodhi, Soumen Maiti, Rajib Chakraborty, and Arnab Panda
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Materials science ,Silicon ,business.industry ,Energy conversion efficiency ,chemistry.chemical_element ,Grating ,Atomic and Molecular Physics, and Optics ,law.invention ,Optics ,Solar cell efficiency ,chemistry ,Active solar ,law ,Solar cell ,Wafer ,Electrical and Electronic Engineering ,Thin film ,business ,Engineering (miscellaneous) - Abstract
Enhancement of optical to electrical conversion is vital for improving the efficiency of any solar cell. In recent years, use of thin films instead of bulk wafers has resulted in a huge reduction of production cost, and as such, efficiency enhancement of thin-film solar cells is considered in this study. Though this enhancement depends on several factors, most significant among them is the increase in light absorption within the active material of the solar cell. In this work, various types of grating structures on both sides of active solar cell material for light trapping are studied in detail, and a new type of arrangement of optimized grating structure that significantly improves the light absorption is selected. Enhancement of light absorption for change in dielectric material of the grating structure without changing the active material is also observed. Along with structural optimization, simulated electrical characterization of the samples was also performed, which yields a short-circuit current density of 29.27 m A / c m 2 with conversion efficiency of 14.51%, having a fill factor of 0.83 for a typical ultrathin layer of active material of thickness 2 µm. This is quite significant because typical cells of this category have much lesser conversion efficiency.
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- 2020
14. Systematics of smectite hydrogen-isotope composition: Structural hydrogen versus adsorbed water
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Arkadiusz Derkowski, Fred J. Longstaffe, Nadine J. Kanik, and Artur Kuligiewicz
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Adsorption ,Hydrogen ,Geochemistry and Petrology ,Chemistry ,Yield (chemistry) ,Inorganic chemistry ,Enthalpy ,chemistry.chemical_element ,Geology ,Composition (visual arts) ,Sample preparation ,Fractionation ,Clay minerals - Abstract
Atmospheric water adsorbed onto clay mineral surfaces, of smectite group minerals in particular, can contaminate hydrogen released from structural hydroxyl groups during hydrogen-isotope analysis. Interlayer cation composition and cation hydration enthalpy, in particular, can affect the magnitude of this excess hydrogen yield and hence the hydrogen isotope composition (δ2H) of smectites. To evaluate this problem, δ2H of different cation-saturated (Ca2+, Na+, K+), dried forms of six smectite standards from the Clay Minerals Society Source Clays were measured using a modified sample drying and on-line High-Temperature-Conversion-Elemental-Analysis (TCEA) Continuous-Flow-Isotope-Ratio-Mass-Spectrometry (CF-IRMS) protocol. More negative interlayer cation hydration enthalpies (Ca2+ > Na+ > K+) led to higher residual adsorbed water contents, which produced poorer δ2H reproducibility for the determination of smectite hydroxyl hydrogen. The lowest adsorbed water contribution and the most reproducible and possibly accurate δ2H for smectite hydroxyl hydrogen was obtained for K-saturated smectites dried for both 4 and 24 h at 220 °C prior to isotopic analysis and transferred to a “Zero-Blank” autosampler in ≤2.5 min. This approach provided the lowest measurement error for hydroxyl δ2H and facilitated much greater sample throughput than classical methods for smectitic clays. This study proposes a protocol for hydroxyl δ2H determination in smectitic clay minerals, and reveals the effect of H-isotope fractionation of adsorbed water during sample preparation.
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- 2022
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15. Extraction of amino acids using supercritical carbon dioxide forin situastrobiological applications
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Isik Kanik, Marlen R. Menlyadiev, Fang Zhong, Ying Lin, and Bryana L. Henderson
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Supercritical carbon dioxide ,Chromatography ,010504 meteorology & atmospheric sciences ,Physics and Astronomy (miscellaneous) ,Extraction (chemistry) ,Mass spectrometry ,01 natural sciences ,Solvent ,Perchlorate ,chemistry.chemical_compound ,Capillary electrophoresis ,chemistry ,Space and Planetary Science ,0103 physical sciences ,Earth and Planetary Sciences (miscellaneous) ,Martian regolith simulant ,010303 astronomy & astrophysics ,Pyrolysis ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Abstract
The detection of organic molecules that are indicative of past or present biological activity within the Solar System bodies and beyond is a key research area in astrobiology. Mars is of particular interest in this regard because of evidence of a (perhaps transient) warm and wet climate in its past. To date, space missions to Mars have primarily used pyrolysis technique to extract organic compounds from the Martian regolith, but it has not enabled a clear detection of unaltered native Martian organics. The elevated temperatures required for pyrolysis extraction can cause native Martian organics to react with perchlorate salts in the regolith, possibly resulting in the chlorohydrocarbons that have been detected by mass spectrometry, a commonly usedin situtechnique for space applications. Supercritical carbon dioxide (SCCO2) extraction technique is a powerful alternative to pyrolysis that may be capable of extracting and delivering unaltered native organic species to an analyser. In this study, we report the SCCO2extraction of unaltered amino acids (AAs) with simple laboratory analyses of extracts by capillary electrophoresis laser-induced fluorescence (CE/LIF) and liquid chromatography with mass spectrometry (LC/MS) techniques. The extraction efficiencies of several representative AAs using SCCO2with small amounts of pure water (~1–5%) as a co-solvent were determined. Glass beads were used as a model substrate to examine the effects of several experimental parameters and Johnson Space Center (JSC) Mars-1A Martian regolith simulant was used to study the effect of complex matrix on extraction efficiencies. With optimized experimental conditions (75C and 5% of water), extraction efficiencies from doped JSC Mars-1A were found to be ~40% for glycine, alanine and serine and ~10% for lysine. Extraction of native organics from undoped JSC Mars-1A suggests that SCCO2/water solvent system can extract both organics extractable with pure SCCO2and those extractable with pure water. Additionally, species not extracted by either pure SCCO2or pure water were extracted with SCCO2/water solvent. Despite the preliminary nature of this work, it paves the path for more comprehensive extraction studies of astrobiologically relevant samples with thorough analyses of resulting extracts.
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- 2018
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16. Relevance between clinical status and exhaled molecules related to neutrophilic inflammation in pediatric cystic fibrosis
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Esra Toprak Kanik, Hasan Yuksel, Ozge Yilmaz, Hüdaver Alper, Cevval Ulman, Ece Ozdogru, Yurda Simsek, Ali Kanik, and Ege Üniversitesi
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Male ,Pulmonary and Respiratory Medicine ,Spirometry ,medicine.medical_specialty ,Leukotriene B4 ,Lung injury ,01 natural sciences ,Gastroenterology ,cystic fibrosis ,03 medical and health sciences ,FEV1/FVC ratio ,chemistry.chemical_compound ,0302 clinical medicine ,Pseudomonas infection ,Internal medicine ,medicine ,Humans ,Exhaled breath condensate ,Child ,IL-8 ,biology ,medicine.diagnostic_test ,business.industry ,010401 analytical chemistry ,medicine.disease ,respiratory tract diseases ,0104 chemical sciences ,IL-17 ,Breath Tests ,030228 respiratory system ,chemistry ,inflammation ,Neutrophil elastase ,LTB4 ,biology.protein ,Sputum ,Female ,medicine.symptom ,business ,neutrophil elastase ,e-cadherin - Abstract
Introduction:Cystic fibrosis (CF) is characterized with chronic inflammation with neutrophil and related cytokines in airway secretions. We aimed to measure the levels of neutrophil related inflammatory markers as nitric oxide, IL-8, IL-17, leukotriene B4 and neutrophil elastase as well as e-cadherin in exhaled breath condensate (EBC), and to determine their relation with clinical findings.Methods:We consecutively enrolled cystic fibrosis patients into our clinics between the age of six and eighteen years who could cooperate for exhaled breath condensate to this case-control study (n = 30). the age and sex matched control group (n = 26) was enrolled. Spirometry was performed during the stable period and EBC samples were obtained for measurement of the markers.Results:The mean age of the subjects enrolled was 12.1(4.2) years and 40% were positive forP.Aeruginosain sputum. Subjects who hadP.Aeruginosain sputum cultures had significantly lower FEV1, FVC and FEF 25/75 values compared to the ones withoutP.Aeruginosa(p = 0.002, p = 0.002 and p = 0.005 respectively). EBC neutrophil elastase levels were significantly higher in the CF patients compared to non-CF controls (3.11 4.71 versus 0.90 2.68, p = 0.04). Nitric oxide, IL-17, IL-8, e-cadherin, neutrophil elastase or leukotriene B4 levels in EBC of CF patients were not related toP.Aeruginosas infection, FEV1 levels or hospital admission in the last year.Conclusion:In our study, neutrophil elastase levels in EBC are higher in CF patients compared to non-CF controls. This is independent of acute infection and is evidence to the persistence of neutrophilic lung injury. However, EBC NO, IL-8, IL-17, e-cadherin, neutrophil elastase and leukotriene B4 levels as inflammatory markers, are not correlated with disease progression or clinical findings.
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- 2020
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17. Highly Sensitive and Label-free Digital Detection of Whole Cell E. coli with Interferometric Reflectance Imaging
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Fulya Ekiz Kanik, Negin Zaraee, Matthew T. Geib, Julia R. Dupuis, Nese Lortlar Ünlü, M. Selim Ünlü, Abdul Bhuiya, Emily Gong, and Ayca Yalcin Ozkumur
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Biomedical Engineering ,Biophysics ,Biosensing Techniques ,02 engineering and technology ,medicine.disease_cause ,01 natural sciences ,Limit of Detection ,Escherichia coli ,Electrochemistry ,medicine ,Humans ,Escherichia coli Infections ,Label free ,Detection limit ,biology ,Chemistry ,Optical Imaging ,010401 analytical chemistry ,Biomolecules (q-bio.BM) ,Pathogenic bacteria ,Equipment Design ,General Medicine ,021001 nanoscience & nanotechnology ,biology.organism_classification ,Reflectivity ,Bacterial Load ,0104 chemical sciences ,Interferometry ,Quantitative Biology - Biomolecules ,FOS: Biological sciences ,0210 nano-technology ,Biological system ,Biosensor ,Bacteria ,Biotechnology - Abstract
Bacterial infectious diseases are a major threat to human health. Timely and sensitive pathogenic bacteria detection is crucial in identifying the bacterial contaminations and preventing the spread of infectious diseases. Due to limitations of conventional bacteria detection techniques there have been concerted research efforts towards development of new biosensors. Biosensors offering label free, whole bacteria detection are highly desirable over those relying on label based or pathogenic molecular components detection. The major advantage is eliminating the additional time and cost required for labeling or extracting the desired bacterial components. Here, we demonstrate rapid, sensitive and label free E. coli detection utilizing interferometric reflectance imaging enhancement allowing for visualizing individual pathogens captured on the surface. Enabled by our ability to count individual bacteria on a large sensor surface, we demonstrate a limit of detection of 2.2 CFU/ml from a buffer solution with no sample preparation. To the best of our knowledge, this high level of sensitivity for whole E. coli detection is unprecedented in label free biosensing. The specificity of our biosensor is validated by comparing the response to target bacteria E. coli and non target bacteria S. aureus, K. pneumonia and P. aeruginosa. The biosensor performance in tap water also proves that its detection capability is unaffected by the sample complexity. Furthermore, our sensor platform provides high optical magnification imaging and thus validation of recorded detection events as the target bacteria based on morphological characterization. Therefore, our sensitive and label free detection method offers new perspectives for direct bacterial detection in real matrices and clinical samples., 15 pages, 6 figures, 1 table
- Published
- 2019
18. Modulation of host lipid membrane elasticity and dipole potential induced by bacterial membrane vesicles
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Deepak Kumar Sinha, Anuj Tiwari, Ashutosh Prince, Nikhil Kanik, Kuldeep Sharma, Titas Mandal, and Mohammed Saleem
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Host cell membrane ,chemistry.chemical_compound ,Membrane ,chemistry ,Phosphatidylcholine ,Phagosome maturation ,Biophysics ,Virulence ,Phosphatidylinositol ,Lipid bilayer ,Virulence factor - Abstract
Bacterial membrane vesicles (MVs) facilitate long-distance delivery of virulence factors crucial for pathogenicity. The entry and trafficking mechanisms of virulence factors inside host cells is recently emerging, however, if bacterial MVs modulate the physicochemical properties of the host lipid membrane remains unknown. Here we reconstitute the interaction of bacterial MV with host cell lipid membranes and quantitatively show that bacterial MV interaction increases the fluidity, dipole potential and elasticity of a biologically relevant multi-component host membrane. The presence of cylindrical lipids such as phosphatidylcholine and phosphatidylinositol and a moderate acyl chain length of C16 helps the MV interaction. While significant binding of bacterial MVs to the raft-like lipid membranes with phase separated regions of the membrane was observed, however, MVs have a preference for binding to the liquid disordered regions of the membrane. Further, the elevated levels of cholesterol tend to hinder the interaction of bacterial MVs. We further quantify the change in excess Gibbs free energy of mixing of bacterial MVs with host lipid membranes driving the modulation of host membrane parameters. The findings may have significant implications on the regulation of host machineries by pathogen through manipulation of host membrane properties.Significance StatementBacterial membrane vesicles (MVs) act as the long-distance delivery tools for virulence factor and thus, directly implicated in host-pathogen interactions and pathogenicity. While the mechanisms of virulence transfer is only recently emerging, however, the interaction of MVs the host cell membrane remains largely unexplored. Whether the MVs interaction can locally modulate the host lipid membrane physicochemical properties (such as fluidity, dipole potential and elasticity) remains unknown. Here, we quantitatively investigate the lipid specificity of E. Coli MV interaction and this results in increase in the fluidity, dipole potential and in-plane elasticity of a biologically relevant multi-component host membrane. The findings could be important for numerous cell-signaling processes as well as downstream events involving membrane-membrane fusion during process of phagosome maturation.
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- 2019
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19. Online supercritical fluid extraction and chromatography of biomarkers analysis in aqueous samples for in situ planetary applications
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Bryana L. Henderson, Ying Lin, Fang Zhong, Victor Abrahamsson, and Isik Kanik
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Detection limit ,Chromatography ,Aqueous solution ,Chemistry ,Electrospray ionization ,010401 analytical chemistry ,Extraction (chemistry) ,Supercritical fluid extraction ,Planets ,Chromatography, Supercritical Fluid ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Analytical Chemistry ,chemistry.chemical_compound ,Supercritical fluid chromatography ,Humans ,0210 nano-technology ,Derivatization ,Quadrupole mass analyzer ,Biomarkers - Abstract
Sensitive and robust in situ chemical analysis of organic biomarkers is essential in the endeavor of finding chemical signatures of life either extinct or extant on our solar system bodies such as Europa, Enceladus, or Titan. Development of new analytical instruments and accompanying methodologies are needed, especially those that are compatible with unknown and diverse samples potentially found on solar system targets and that avoid complexities involved with other wet chemistry techniques (desalting, derivatization and contamination issues, etc.). In this study, we demonstrate that online supercritical fluid extraction and supercritical fluid chromatography with water-saturated CO2 can extract and separate nonpolar analytes of astrobiological interest, such as free fatty acids, polycyclic aromatic hydrocarbons, and polycyclic aromatic compounds containing nitrogen or sulfur. Silica was used as a support material to immobilize aqueous samples during extraction. A C18 stationary phase with an embedded polar functional group and efficient end-capping in combination with water in the mobile phase allowed efficient separation of both free fatty acids and basic compounds. The total analysis time was 30 min, including extraction, equilibration, and separation. Detection was performed with a UV detector and a quadrupole mass spectrometer equipped with electrospray ionization. The method was validated in terms of lower detection limits (0.02–40 μg/L), precision (repeatability 3–13%), relative standard deviation (RSD), intermediate precision 4–26% (RSD), trueness (bias ranging from − 48 to 9%), and retention time shifts (
- Published
- 2019
20. Effect of fixation conditions on yellowing behavior of cellulose powder-coated fabrics
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Kenan Yildirim, Gizem Manasoglu, Mehmet Kanik, and Yıldırım, Kenan
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Thermogravimetric analysis ,Materials science ,thermal gravimetric analysis ,02 engineering and technology ,engineering.material ,010402 general chemistry ,01 natural sciences ,Cellulose Powders ,chemistry.chemical_compound ,Fixation (surgical) ,Coating ,General Materials Science ,textile coating ,Cellulose ,Fourier transform infrared spectroscopy ,Composite material ,Cellulose powder ,technology, industry, and agriculture ,yellowing ,temperature ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Polyester ,chemistry ,engineering ,0210 nano-technology - Abstract
WOS:000459759500001 In this study, the yellowing behavior of cellulose powders, which is applied to pretreated polyester woven fabrics with concentrations of 100g/kg by knife coating technique, was investigated. After drying process, coated fabrics were cured at different conditions to determine the effects of the curing temperature and time on yellowing behaviors. The yellowness-whiteness of coated fabrics was measured with a spectrophotometer according to ASTM E313. As the curing temperature and time increase, yellowing effect was more observable. However, the effect of temperature increase is found to be more significant than the increase in curing duration in terms of more observed yellowness. In order to investigate the reason of yellowing, cellulose powder samples were heated in drying oven at three different heating temperatures (130 degrees C, 150 degrees C, and 170 degrees C) for three different heating periods (3, 5, and 7 min). Then, thermal gravimetric analysis and Fourier transform infrared spectroscopy analysis of powder samples were performed for each temperature-period combinations. No ring-opening reaction on the cellulose group was found in the Fourier transform infrared spectroscopy analysis. However, the changes in the spectra can be attributed to the chain breakage in the cellulose macromolecules as well as water loss from the molecular structure during the heating process. Microscopic and scanning electron microscopic analysis was carried out to see any surface change on the fiber and coated fabric. There was no detectable surface change on the fiber and coated fabric surface, apart from a color change on the fabric surface.
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- 2019
21. Supercritical Carbon Dioxide Extraction of Coronene in the Presence of Perchlorate forIn SituChemical Analysis of Martian Regolith
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Ying Lin, Isik Kanik, Shirley Y. Chung, H. C. McCaig, Amanda M. Stockton, Fang Zhong, and Candice Crilly
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Geologic Sediments ,Extraterrestrial Environment ,010504 meteorology & atmospheric sciences ,Mars ,Polycyclic aromatic hydrocarbon ,01 natural sciences ,chemistry.chemical_compound ,Perchlorate ,0103 physical sciences ,Polycyclic Compounds ,010303 astronomy & astrophysics ,0105 earth and related environmental sciences ,Martian ,chemistry.chemical_classification ,Perchlorates ,Supercritical carbon dioxide ,Chemistry ,Extraction (chemistry) ,Temperature ,Carbon Dioxide ,Sodium Compounds ,Agricultural and Biological Sciences (miscellaneous) ,Regolith ,Microspheres ,Coronene ,Spectrometry, Fluorescence ,Space and Planetary Science ,Environmental chemistry ,Salts ,Glass ,Pyrolysis - Abstract
The analysis of the organic compounds present in the martian regolith is essential for understanding the history and habitability of Mars, as well as studying the signs of possible extant or extinct life. To date, pyrolysis, the only technique that has been used to extract organic compounds from the martian regolith, has not enabled the detection of unaltered native martian organics. The elevated temperatures required for pyrolysis extraction can cause native martian organics to react with perchlorate salts in the regolith and possibly result in the chlorohydrocarbons that have been detected by in situ instruments. Supercritical carbon dioxide (SCCO2) extraction is an alternative to pyrolysis that may be capable of delivering unaltered native organic species to an in situ detector. In this study, we report the SCCO2 extraction of unaltered coronene, a representative polycyclic aromatic hydrocarbon (PAH), from martian regolith simulants, in the presence of 3 parts per thousand (ppth) sodium perchlorate. PAHs are a class of nonpolar molecules of astrobiological interest and are delivered to the martian surface by meteoritic infall. We also determined that the extraction efficiency of coronene was unaffected by the presence of perchlorate on the regolith simulant, and that no sodium perchlorate was extracted by SCCO2. This indicates that SCCO2 extraction can provide de-salted samples that could be directly delivered to a variety of in situ detectors. SCCO2 was also used to extract trace native fluorescent organic compounds from the martian regolith simulant JSC Mars-1, providing further evidence that SCCO2 extraction may provide an alternative to pyrolysis to enable the delivery of unaltered native organic compounds to an in situ detector on a future Mars rover.Biomarkers-Carbon dioxide-In situ measurement-Mars-Search for Mars' organics. Astrobiology 16, 703-714.
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- 2016
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22. Targeting MYD88-Mutant DLBCL with IRAKIMiDs: A Comparison to IRAK4 Kinase Inhibition and Evaluation of Synergy with Rational Combinations
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Owen A. O'Connor, Duncan Walker, André M. Grilo, Alice McDonald, Jennifer K. Lue, Nello Mainolfi, John S Manavalan, Rahul Kanik, Jared Gollob, and Christine Klaus
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Chemistry ,Immunology ,Mutant ,Cancer research ,Cell Biology ,Hematology ,Kinase inhibition ,IRAK4 ,Biochemistry - Abstract
Introduction: MYD88 mutations are found in 25% of DLBCL and are associated with an inferior survival. MYD88 is an adapter molecule, forming the core of the Myddosome complex. MYD88 mutations constitutively activate pathways such as NFқB, leading to lymphomagenesis. Essential to the Myddosome-dependent signaling pathway is the recruitment of IRAK4 which complexes with MYD88 to activate downstream effects. Targeting IRAK4 is therefore a rational therapeutic approach in MYD88-mutant lymphomas. First-in-class IRAKIMiDs, novel heterobifunctional degraders that target IRAK4 as well as the IMiD substrates Ikaros and Aiolos to enable the inhibition of both the NFkB and IRF4 pathways activated by MYD88 mutations, demonstrate potent efficacy in MYD88-mutant lymphomas (KTX-475, KTX-582, Walker D et al. AACR 2020). Herein, we compare the activity of IRAKIMiDs to IRAK4 kinase inhibitors and IMiDs alone in MYD88-mutant DLBCL, and evaluate rational combinations of IRAKIMiDs and other active agents in DLBCL for synergy. Methods: MYD88-mutant (n=4) and wild type (n=4) DLBCL cell lines were exposed to a panel of single agents (KTX-475, KTX-582, BAY1830839, CA-4948, CC-220, lenalidomide, pomalidomide, ibrutinib, umbralisib, venetoclax) in order to establish the drug concentration:cytotoxicity effect relationship. Cell viability was assessed using Celltiter-Glo assay at 24-hour intervals. IC50 values were computed. MYD88-mutant DLBCL cells were co-exposed to combinations of KTX-475 with venetoclax, ibrutinib, or umbralisib at concentrations representing their respective IC10-40 in order to determine synergy using the excess over bliss (EOB) method. Venetoclax, ibrutinib, and umbralisib were selected for combinational studies in order to target adverse pathways known to be associated in DLBCL biology. To confirm IRAK4 degradation, western blot and flow cytometry was performed. Apoptosis was evaluated with flow cytometry. Pre-treatment RNA-seq libraries were developed for the purpose of identifying GSEA and mutational analysis to predict response to IRAKIMiDs. Results: Exposure to IRAKIMiDs led to potent activity in MYD88-mutated DLBCL with IC50s in the low nanomolar range. IRAK4 degradation occured in a dose- and time-dependent manner and was observed as early as four hours after exposure. IRAKIMiDs induced superior cytotoxicity compared to two IRAK4 kinase inhibitors, including CA-4948 (Curis), which is currently under clinical investigation for relapsed/refractory NHL, as determined by lower IC50s in all cell lines. IRAKIMiD IC50s were also lower compared to pomalidomide, lenalidomide, and CC-220. KTX-475 was selected for synergy assessments based on IC50 values. Synergy was observed after exposure to KTX-475 in conjunction with venetoclax, ibrutinib, or umbralisib as determined by EOB >0 in the MYD88-mutant OCI-LY10 model, with maximum values peaking at 72-96 hours. After dual drug exposure, IRAK4 degradation was validated by flow cytometry demonstrating that the addition of venetoclax, ibrutinib or umbralisib to KTX-475 did not impair IRAK4 degradation capabilities. RNA-seq interpretation is currently underway. Conclusions: Collectively, our results demonstrate that dual-function degraders targeting both IRAK4 and the IMiD substrates Ikaros and Aiolos can serve as a potential therapeutic option for poor prognosis MYD88-mutant DLBCL. Our data thus far demonstrate improved efficacy of IRAKIMiDs compared to IRAK4 kinase inhibitors or IMiDs alone in vitro, as well as synergy with other active agents in combination regimens. A promising lead IRAKIMiD candidate has been identified, with initiation of a first-in-human clinical trial in B-cell lymphomas planned for 2021. Disclosures Lue: Daiichi Sankyo: Honoraria; AstraZeneca: Speakers Bureau; Astex Pharmaceuticals: Honoraria; Kymera Therapeutics: Honoraria, Research Funding; Kura Oncology: Honoraria. Klaus:Kymera Therapeutics: Current Employment, Current equity holder in publicly-traded company. Kanik:Kymera Therapeutics: Current Employment, Current equity holder in publicly-traded company. McDonald:Kymera Therapeutics: Current Employment, Current equity holder in publicly-traded company. Gollob:Kymera Therapeutics: Current Employment, Current equity holder in publicly-traded company. Walker:Kymera Therapeutics: Current Employment, Current equity holder in publicly-traded company. O'Connor:Kymera Therapeutics: Current equity holder in private company, Honoraria, Membership on an entity's Board of Directors or advisory committees; TG Therapeutics: Current Employment, Current equity holder in publicly-traded company; Servier: Consultancy; Mundipharma: Other: Consulting; Astex Pharmaceuticals: Honoraria, Research Funding; Merck: Research Funding; Nomocan: Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Other: Data Safety Monitoring Committee, Research Funding. Mainolfi:Kymera Therapeutics: Current Employment, Current equity holder in publicly-traded company.
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- 2020
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23. A digital microarray for transcriptional biomarkers of antibiotic resistance utilizing plasmonic nanorods and interferometric imaging (Conference Presentation)
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M. Selim Ünlü, George G. Daaboul, Derin Sevenler, Ahmad S. Khalil, Fulya Ekiz Kanik, Joseph Greene, and Emma Briars
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Antibiotic resistance ,Microarray ,law ,Chemistry ,Gene expression ,IRIS (biosensor) ,Computational biology ,Lab-on-a-chip ,DNA microarray ,Interferometric microscopy ,Biosensor ,law.invention - Abstract
The standard laboratory procedure for determining the antibiotic susceptibility of a pathogen (an antimicrobial susceptibility test, AST) measures the inhibition of growth, and requires several days. This can delay effective therapy and lead to antibiotic overuse and misuse. Recent work (Wei Hou et al, Lab on a Chip 2015) has shown that resistant and susceptible pathogens will have very different gene expression profiles shortly following antibiotic exposure, and that these expression biomarkers may be used to accurately identify the pathogen species, strain and antibiotic susceptibility without growth. We therefore developed an ultrasensitive ‘digital microarray’ for performing rapid & quantitative gene expression analysis as part of a rapid AST. The digital microarray uses plasmonic gold nanorods (GNRs) functionalized with DNA to specifically label each target RNA that binds to the microarray. Each GNR on the array is then individually detected based on its light scattering, with an interferometric microscopy technique called SP- IRIS. Our optimized high-throughput version of SP-IRIS is able to scan a typical array of 500 spots in less than 10 minutes. Due to its single molecule readout, the assay has a limit of detection of less than 1 femtomolar following just 2 hours of incubation. Altogether, digital microarrays are about 10,000-fold more sensitive than fluorescence microarrays, yet maintain all of the strengths of the platform including low cost and high multiplexing. The reproducibility and robustness of the multiplexed assay will next be evaluated with clinically relevant pathogenic strains of E. coli as part of a functional rapid AST.
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- 2018
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24. Mackinawite and greigite in ancient alkaline hydrothermal chimneys: Identifying potential key catalysts for emergent life
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Galen D. Stucky, Michael J. Russell, Lauren M. White, Isik Kanik, and Rohit Bhartia
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Greigite ,biology ,Geochemistry ,Iron sulfide ,engineering.material ,Early Earth ,Hydrothermal circulation ,chemistry.chemical_compound ,Geophysics ,Chemical engineering ,Mackinawite ,chemistry ,Space and Planetary Science ,Geochemistry and Petrology ,Abiogenesis ,Earth and Planetary Sciences (miscellaneous) ,engineering ,biology.protein ,Geology ,Carbon monoxide dehydrogenase ,Hydrothermal vent - Abstract
One model for the emergence of life posits that ancient, low temperature, submarine alkaline hydrothermal vents, partly composed of iron-sulfides, were capable of catalyzing the synthesis of prebiotic organic molecules from CO2, H2 and CH4. Specifically, hydrothermal mackinawite (FeIIS) and greigite (FeIIFeIII2S4) have been highlighted in previous studies as analogs of the active centers of hydrogenase, ferredoxin, acetyl coenzyme-A synthase and carbon monoxide dehydrogenase featured in the biochemistry of certain autotrophic prokaryotes that occupy the base of the evolutionary tree. Despite the proposed importance of iron sulfide minerals and clusters in the synthesis of abiotic organic molecules, the mechanisms for the formation of these sulfides from solution and their preservation under the anoxic and low temperature (below 100 °C) conditions expected in off-axis submarine alkaline vent systems is not well understood ( Bourdoiseau et al., 2011 , Rickard and Luther, 2007 ). To rectify this, single hydrothermal chimneys were precipitated using a unique apparatus to simulate growth at hydrothermal vents of moderate temperature under supposed Hadean ocean-bottom conditions. Iron sulfide phases were observed through Raman spectroscopy at growth temperatures ranging from 40° to 80 °C. Fe(III)-containing mackinawite is confirmed to be present with mackinawite and greigite, supporting an FeIII-mackinawite intermediate mechanism for the transformation of mackinawite to greigite below 100 °C. Raman spectroscopy of the chimneys revealed a maximum yield of greigite at 75 °C. These results suggest abiotic production of catalytically active mackinawite and greigite are possible under early Earth hydrothermal conditions as well as on other wet, rocky worlds geochemically similar to the Earth.
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- 2015
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25. Wpływ wybranych zagrożeń środowiskowych na właściwości hydrofobowe drobnodyspersyjnego wapienia / The Influence of Chosen Environmental Hazards on Hydrophobic Properties of Fine Dispersional Limestone
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Eliza Wolak, Anna Horak, Elżbieta Vogt, and Urszula Kanik
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chemistry.chemical_classification ,Cement ,Materials science ,Base (chemistry) ,Metallurgy ,Humidity ,engineering.material ,Raw material ,Bulk density ,chemistry.chemical_compound ,chemistry ,engineering ,Hydroxide ,Stearic acid ,Lime - Abstract
Streszczenie Przestawiono wyniki badań zmiany hydrofobowych właściwości drobnodyspersyjnego wapienia pod wpływem wybranych czynników korozyjnych. Badano dwie frakcje ziarnowe drobnodysper- syjnego wapienia, o średnicy ziaren zgodnie z danymi producenta (Kopalnia Wapienia Czatkowice) wynoszącej odpowiednio: dla mączki wapiennej poniżej 80 um oraz piasku wapiennego z przedziału 100-400 um. Badano również mączką wapienną hydrofobizowaną w kamieniołomie wapieni i margli cementowni w Małogoszczy. Badano materiały surowe oraz hydrofobizowanc za pomocą kwasu stearynowego, preparatu silikonowego oraz preparatu bitumicznego. Jako substancji agresywnych (korodotwórczych) użyto roztworów: kwasu etanowego, zasady amonowej, siarczanu VI sodu. Określono wpływ tych substancji na zmianą nasiąkliwości i ściśliwości badanych materiałów. Miarą nasiąkliwości była zmiana wilgotności materiałów podczas procesu wilgotnego składowania. Ściśli- wość obliczano na podstawie pomiarów deasymetrycznych: gęstości nasypowej swobodnej i upako- wanej, oznaczanych za pomocą cylindra miarowego. Niewielkie zmiany wartości współczynników ściśliwości uzyskane dla materiałów skorodowanych w porównaniu do wartości uzyskanych dla materiałów wyjściowych świadczą o podobnych właściwościach kohezyjnych obu rodzajów mate- riałów. Większość modyfikowanych (hydrofobowych) materiałów po procesie korodowania uzyski- wała gorsze właściwości wodoodporne niż materiały wyjściowe, ale w dalszym ciągu charakte- ryzowała sią wyższym stopniem hydrofobowości niż skorodowane materiały surowe. Dla mączki wapiennej nie uzyskano powtarzalnych wyników, co najprawdopodobniej spowodowane jest większą reaktywnością tego materiału związaną z małą średnicą ziaren. Przeprowadzone badania miały charakter wstępny.
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- 2015
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26. From Chemical Gardens to Fuel Cells: Generation of Electrical Potential and Current Across Self-Assembling Iron Mineral Membranes
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Julyan H. E. Cartwright, Laura M. Barge, Isik Kanik, Ivria J. Doloboff, Michael J. Russell, Richard D. Kidd, and Yeghegis Abedian
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Chemistry ,Electric potential energy ,Inorganic chemistry ,Nanotechnology ,General Chemistry ,General Medicine ,Electrochemistry ,Electrochemical energy conversion ,Redox ,Catalysis ,Hydrothermal circulation ,Membrane ,Chemical garden ,Current (fluid) - Abstract
We examine the electrochemical gradients that form across chemical garden membranes and investigate how self-assembling, out-of-equilibrium inorganic precipitates—mimicking in some ways those generated in far-from-equilibrium natural systems—can generate electrochemical energy. Measurements of electrical potential and current were made across membranes precipitated both by injection and solution interface methods in iron-sulfide and iron-hydroxide reaction systems. The battery-like nature of chemical gardens was demonstrated by linking multiple experiments in series which produced sufficient electrical energy to light an external light-emitting diode (LED). This work paves the way for determining relevant properties of geological precipitates that may have played a role in hydrothermal redox chemistry at the origin of life, and materials applications that utilize the electrochemical properties of self-organizing chemical systems.
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- 2015
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27. Preparation and Characterization of a Novel Solid-Phase Microextraction Material for Application to the Determination of Pesticides
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F. Nil Ertaş, Levent Pelit, Korcan Korba, Füsun Okçu Pelit, Levent Toppare, Tugberk Nail Dizdas, Hasan Ertaş, and Fulya Ekiz Kanik
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Thermogravimetric analysis ,Chromatography ,Chemistry ,010401 analytical chemistry ,Biochemistry (medical) ,Clinical Biochemistry ,Extraction (chemistry) ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Solid-phase microextraction ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Analytical Chemistry ,Electron capture detector ,Adsorption ,Desorption ,Electrochemistry ,Fiber ,Gas chromatography ,0210 nano-technology ,Spectroscopy - Abstract
The preparation and characterization of a novel solid-phase microextraction fiber is reported with application to the determination of pesticides in fruit juice. The fiber was fabricated by electrochemically coating a stainless steel wire with a thin polymeric film of 4-(2,5-di(thiophen-2-yl)-1H-pyrrol-1-yl) benzenamine. The procedure was initiated in 10 mL of acetonitrile containing 5.5 mg of monomer, 0.1 mol NaClO4, and 0.1 mol LiClO4 by cycling the potential between −0.5 and 1.2 V with a scan rate of 100 mV/sec. The morphology of the fiber surface was examined by scanning electron microscopy and its stability was characterized by thermal gravimetric analysis. The fiber was exposed to headspace extraction of bromopropylate, chlorpyrifos, lambda-cyhalothrin, penconazole, and procymidone prior to the analysis by gas chromatography with an electron capture detector. Operational parameters affecting the extraction efficiency, adsorption and desorption times and temperature, and stirring rate were sc...
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- 2015
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28. Relationship with Loss of SIGLEC14 and the Risk of COPD Exacerbation
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Arzu Kanik, Mukadder Calikoğlu, Esin Tastekin, and Lülüfer Tamer
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COPD ,Exacerbation ,business.industry ,Sialic acid binding ,medicine.disease ,medicine.disease_cause ,Sialic acid ,Haemophilus influenzae ,chemistry.chemical_compound ,chemistry ,Polymorphism (computer science) ,Immunology ,Genotype ,medicine ,Gene polymorphism ,business - Abstract
COPD is a chronic inflammatory disease which usually resulting from gene-environment interaction and complex, heterogeneous and characterized by exacerbations. NTHi (typeable Haemophilus influenzae) is the major known cause of COPD exacerbations and express sialic acid which contain lipooligosakkarit. There are some claims that Siglec-14, which is one of the sialic acid binding from lectins, increases immune cells of the inflammatory by interacting with the NTHi and causes more frequently to the exacerbations of COPD. In our study, it was aimed to determine relationship between exacerbations and SIGLEC-14 gene polymorphism in patients with COPD. Our study is a prospective comparative case series study which includes healthy controls. 85 COPD patients and for control group 94 healthy which was evaluated by Mersin University of Medicine Faculty Hospital pulmonary clinic with diagnosis of COPD between june 2015-june 2016 where included in our study. These SIGLEC14 genotype of DNA samples from venous blood and plasma were evaluated in Siglec-14 concentration and the patients monitored for exacerbation during a year. In both groups, SIGLEC14 wild / wild polymorphism is dominant, in patients group SIGLEC14 null / null polymorphism was not observed. The patients who have SIGLEC 14 wild / wild number of exacerbations was significantly greater (p = 0.041) than the patients who have SIGLEC14 wild/null genotipe. In adition the number of exacerbations in this group of patients receiving ICS was significantly higher than patients in the SIGLEC14 wild / null genotype (p=0.012). Ultimately, SIGLEC14 wild/wild polymorphism may be a predictor of exacerbations in COPD, but the same can not be said for SIGLEC14 serum levels.
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- 2017
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29. Bio-Inspired Hierarchically Structured Polymer Fibers For Anisotropic Non-Wetting Surfaces
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Mehmet Kanik, Urandelger Tuvshindorj, Adem Yildirim, Mehmet Bayindir, Fahri Emre Ozturk, Muhammad Yunusa, and Bayındır, Mehmet
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Materials science ,Superhydrophobicity ,General Chemical Engineering ,Surface treatment ,Mixing (process engineering) ,Nanoparticle ,Physics::Optics ,Nanotechnology ,Wetting ,02 engineering and technology ,010402 general chemistry ,Inherent flexibility ,01 natural sciences ,Anisotropic behaviors ,Physics::Fluid Dynamics ,Fiber architecture ,Nano ,Fiber ,Texture (crystalline) ,Anisotropy ,Structured polymers ,chemistry.chemical_classification ,General Chemistry ,Polymer ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Fibers ,Condensed Matter::Soft Condensed Matter ,chemistry ,Non-wetting properties ,Surface modification ,Nanoparticles ,Organically modified silica ,0210 nano-technology ,Nanoparticle surface modification - Abstract
We demonstrate a rice leaf-like hierarchically textured polymer fiber array for anisotropic non-wetting surfaces. To provide superhydrophobicity in addition to the anisotropic behavior, fiber surfaces are spray coated with organically modified silica nanoparticles. The resulting micro/nano hierarchically structured fiber surfaces demonstrate anisotropic non- wetting properties. We designed various fiber architectures for droplet transportation, mixing, and guiding exploiting the scalability of the fiber texture during thermal drawing; optional nanoparticle surface modification; and inherent flexibility of the fibers.
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- 2017
30. Surface chemistry and morphology in single particle optical imaging
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Nese Lortlar Ünlü, M. Selim Ünlü, Derin Sevenler, Marcella Chiari, and Fulya Ekiz-Kanik
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0301 basic medicine ,Surface (mathematics) ,Morphology (linguistics) ,QC1-999 ,Nanoparticle ,02 engineering and technology ,Tracking (particle physics) ,Nanomaterials ,optical biosensors ,03 medical and health sciences ,surface morphology ,Electrical and Electronic Engineering ,Surface plasmon resonance ,Chemistry ,business.industry ,Physics ,single-particle detection ,021001 nanoscience & nanotechnology ,Atomic and Molecular Physics, and Optics ,Electronic, Optical and Magnetic Materials ,030104 developmental biology ,Particle ,Optoelectronics ,Surface modification ,0210 nano-technology ,business ,nanoparticle imaging ,surface modification ,Biotechnology - Abstract
Biological nanoparticles such as viruses and exosomes are important biomarkers for a range of medical conditions, from infectious diseases to cancer. Biological sensors that detect whole viruses and exosomes with high specificity, yet without additional labeling, are promising because they reduce the complexity of sample preparation and may improve measurement quality by retaining information about nanoscale physical structure of the bio-nanoparticle (BNP). Towards this end, a variety of BNP biosensor technologies have been developed, several of which are capable of enumerating the precise number of detected viruses or exosomes and analyzing physical properties of each individual particle. Optical imaging techniques are promising candidates among broad range of label-free nanoparticle detectors. These imaging BNP sensors detect the binding of single nanoparticles on a flat surface functionalized with a specific capture molecule or an array of multiplexed capture probes. The functionalization step confers all molecular specificity for the sensor’s target but can introduce an unforeseen problem; a rough and inhomogeneous surface coating can be a source of noise, as these sensors detect small local changes in optical refractive index. In this paper, we review several optical technologies for label-free BNP detectors with a focus on imaging systems. We compare the surface-imaging methods including dark-field, surface plasmon resonance imaging and interference reflectance imaging. We discuss the importance of ensuring consistently uniform and smooth surface coatings of capture molecules for these types of biosensors and finally summarize several methods that have been developed towards addressing this challenge.
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- 2017
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31. DNA-Directed Antibody Immobilization for Robust Protein Microarrays: Application to Single Particle Detection ‘DNA-Directed Antibody Immobilization
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Fulya Ekiz Kanik, John H. Connor, M. Selim Ünlü, Nese Lortlar Ünlü, and Elif Seymour
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Analyte ,biology ,Protein immobilization ,Chemistry ,Small volume ,010401 analytical chemistry ,02 engineering and technology ,Computational biology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Reflectivity ,Molecular biology ,0104 chemical sciences ,chemistry.chemical_compound ,Protein microarray ,biology.protein ,Antibody ,0210 nano-technology ,DNA - Abstract
Protein microarrays are emerging tools which have become very powerful in multiplexed detection technologies. A variety of proteins can be immobilized on a sensor chip allowing for multiplexed diagnostics. Therefore, various types of analyte in a small volume of sample can be detected simultaneously. Protein immobilization is a crucial step for creating a robust and sensitive protein microarray-based detection system. In order to achieve a successful protein immobilization and preserve the activity of the proteins after immobilization, DNA-directed immobilization is a promising technique. Here, we present the design and the use of DNA-directed immobilized (DDI) antibodies in fabrication of robust protein microarrays. We focus on application of protein microarrays for capturing and detecting nanoparticles such as intact viruses. Experimental results on Single-particle interferometric reflectance imaging sensor (SP-IRIS) are used to validate the advantages of the DDI method.
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- 2017
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32. Pyrophosphate synthesis in iron mineral films and membranes simulating prebiotic submarine hydrothermal precipitates
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Galen D. Stucky, Isik Kanik, David G. VanderVelde, Laura M. Barge, John Zeytounian, Ivria J. Doloboff, Lauren M. White, Michael J. Russell, Marc M. Baum, and Richard D. Kidd
- Subjects
Pyrophosphatase ,ATP synthase ,biology ,Chemistry ,Chemiosmosis ,Inorganic chemistry ,Iron sulfide ,Pyrophosphate ,Substrate-level phosphorylation ,chemistry.chemical_compound ,Adenosine diphosphate ,Geochemistry and Petrology ,biology.protein ,Adenosine triphosphate - Abstract
Cells use three main ways of generating energy currency to drive metabolism: (i) conversion of adenosine diphosphate (ADP) to adenosine triphosphate (ATP) by the proton motive force through the rotor-stator ATP synthase; (ii) the synthesis of inorganic phosphate∼phosphate bonds via proton (or sodium) pyrophosphate synthase; or (iii) substrate-level phosphorylation through the direct donation from an active phosphoryl donor. A mechanism to produce a pyrophosphate bond as “energy currency” in prebiotic systems is one of the most important considerations for origin of life research. Baltscheffsky (1996) suggests that inorganic pyrophosphate (P_2O_7^(4-); PP_i) may have preceded ATP/ADP as an energy storage molecule in earliest life, produced by an H^+ pyrophosphatase. Here we test the hypothesis that PP_i could be synthesized in inorganic precipitates simulating hydrothermal chimney structures transected by thermal and/or ionic gradients. Appreciable yields of PP_i were obtained via substrate phosphorylation by acetyl phosphate within the iron sulfide/silicate precipitates at temperatures expected for an alkaline hydrothermal system.
- Published
- 2014
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33. Development of a novel biosensor based on a conducting polymer
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Fulya Ekiz Kanik, Levent Toppare, Merve Ileri, Serife O. Hacioglu, and Saniye Soylemez
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chemistry.chemical_classification ,Conductive polymer ,Cholesterol oxidase ,Cholesterol Oxidase ,Polymers ,Inorganic chemistry ,Analytical chemistry ,Substrate (chemistry) ,Biosensing Techniques ,Polymer ,Enzymes, Immobilized ,Amperometry ,Analytical Chemistry ,Matrix (chemical analysis) ,Cholesterol ,chemistry ,Covalent bond ,Humans ,Graphite ,Biosensor ,Food Analysis - Abstract
A new type of amperometric cholesterol biosensor was fabricated to improve the biosensor characteristics such as sensitivity and reliability. For this purpose, a novel immobilization matrix 2-(4-fluorophenyl)-4,7-di(thiophene-2-yl)-1 H -benzo[ d ]imidazole (BIPF) was electrochemically deposited on a graphite electrode and used as a matrix for the immobilization of cholesterol oxidase (ChOx). Due to strong π–π stacking of aromatic groups in the structures of polymer backbone and enzyme molecule, one can easily achieve a sensitive and reliable biosensor without using any membrane or covalent bond formation between the enzyme molecules and polymer surface. Moreover, through pendant fluorine group of the polymer, H-bond formation between with enzyme molecules and polymer was generated. Cholesterol was used as the substrate and amperometric response was measured in correlation with cholesterol amount, at −0.7 V vs. Ag/AgCl in phosphate buffer (pH 7.0). Consequently, optimum conditions for this constructed biosensor were determined. K M app, I max , LOD and sensitivity values were investigated and calculated as 4.0 nM, 2.27 µA, 0.404 µM and 1.47 mA/mM cm 2 , respectively. A novel and accurate cholesterol biosensor was developed for the determination of total cholesterol in food samples.
- Published
- 2014
- Full Text
- View/download PDF
34. A functional immobilization matrix based on a conducting polymer and functionalized gold nanoparticles: Synthesis and its application as an amperometric glucose biosensor
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Duygu Kozanoglu, Suna Timur, Melis Kesik, Fulya Ekiz Kanik, Levent Toppare, Emren Nalbant Esenturk, and Gonul Hizalan
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chemistry.chemical_classification ,Conductive polymer ,Materials science ,Polymers and Plastics ,biology ,Biomolecule ,Organic Chemistry ,technology, industry, and agriculture ,Nanoparticle ,Nanotechnology ,Polymer ,Amperometry ,chemistry ,Chemical engineering ,Colloidal gold ,Materials Chemistry ,biology.protein ,Glucose oxidase ,Biosensor - Abstract
Combination of nanoparticles and biomolecules attracted considerable attention in biosensing applications. In this study, effective surface design was investigated by modifying the electrode surface with pristine and functionalized gold nanoparticles. For this purpose, spherical gold nanoparticles were synthesized and characterized with UV–vis spectroscopy and transmission electron microscopy (TEM) analyses. Then, gold nanoparticles were modified with mercaptopropionic acid (MPA) yielding Au–S bonds (Au NPs/MPA). Moreover, a novel functional monomer, 6-(4,7-bis(2,3-dihydrothieno [3,4- b ][1,4]dioxin-5-yl)-2 H -benzo[ d ][1,2,3]triazol-2-yl)hexan-1-amine (BEDOA-6), was synthesized and used as an immobilization matrix for glucose biosensor. After successful electrochemical deposition of the polymer; poly(BEDOA-6) on graphite electrodes, immobilization of glucose oxidase (GOx) was carried out covalently with the help of crosslinking agent. During immobilization, Au NPs and Au NPs/MPA were used in biosensor fabrication in order to achieve the most effective surface design for target biosensor. In addition, SEM and fluorescence analyses were utilized to characterize the surface properties. The biosensor shows a wide linear range between 0.025 mM and 1.25 mM glucose concentration with a low detection limit of 0.025 mM. Also, kinetic parameters, operational and storage stabilities were determined. Finally, the biosensor was tested on beverages for glucose detection.
- Published
- 2013
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35. Interfacial reactions of ozone with surfactant protein B in a model lung surfactant system
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Kim, Hugh I., Hyungjun Kim, Young Shik Shin, Beegle, Luther W., Seung Soon Jang, Neidholdt, Evan L., Goddard, William A., Heath, James R., Kanik, Isik, and Beauchamp, J.L.
- Subjects
Hydrophobic effect -- Analysis ,Oxidation-reduction reaction -- Analysis ,Ozone -- Chemical properties ,Surface active agents -- Chemical properties ,Surface active agents -- Structure ,Glycerin -- Chemical properties ,Glycerol -- Chemical properties ,Chemistry - Abstract
Structurally specific oxidative changes of surfactant protein B (SP-[B.sub.1-25]) at the air-liquid interfaces are described along with the interfacial oxidation of SP-[B.sub.1-25] in a nonionizable 1-palmitoyl-2-oleoyl-sn-glycerol (POG) surfactant layer as a model pulmonary surfactant (PS) system. The results have shown that the heterogeneous reaction of SP-[B.sub.1-25] at the interface is different from that in the solution phase and that only a subset of the amino acids known to react with ozone are oxidized by direct ozonolysis in the hydrophobic interfacial environment.
- Published
- 2010
36. Continuous triboelectric power harvesting and biochemical sensing inside poly(vinylidene fluoride) hollow fibers using microfluidic droplet generation
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Caglar Elbuken, Mehmet Kanik, Muhammad Yunusa, Merve Marcali, Mehmet Bayindir, and Bayındır, Mehmet
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Materials science ,PVDF fiber ,Microfluidics ,Nanotechnology ,Triboelectricity ,02 engineering and technology ,macromolecular substances ,010402 general chemistry ,01 natural sciences ,7. Clean energy ,Industrial and Manufacturing Engineering ,chemistry.chemical_compound ,General Materials Science ,Triboelectric effect ,Energy harvesting ,technology, industry, and agriculture ,food and beverages ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Biosensors ,chemistry ,Mechanics of Materials ,Chemical sensors ,0210 nano-technology ,Biosensor ,Fluoride - Abstract
Triboelectric power harvesting and biochemical sensing inside poly(vinylidene fluoride) hollow fibers. Fiber‐based microfluidic energy harvesting system, which is also utilized as self‐powered chemical and biosensor. In vitro device concept demonstrating that triboelectric effect can be used for cell detection.
- Published
- 2016
37. Peptide and RNA contributions to iron–sulphur chemical gardens as life's first inorganic compartments, catalysts, capacitors and condensers
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Michael J. Russell, Shawn E. McGlynn, and Isik Kanik
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Models, Molecular ,Models, Genetic ,Chemistry ,Iron ,General Mathematics ,General Engineering ,General Physics and Astronomy ,Signal Processing, Computer-Assisted ,Electric Capacitance ,Anoxic waters ,Catalysis ,Hydrothermal circulation ,Models, Chemical ,Transition metal ,Chemical engineering ,Inorganic Chemicals ,Abiogenesis ,RNA ,Chimney ,Crystallization ,Peptides ,Sulfur ,Stoichiometry ,Hydrothermal vent - Abstract
Hydrothermal chimneys and compartments comprising transition metal sulphides and associated minerals have been proposed as likely locations for the beginnings of life. In laboratory simulations of off-axis alkaline springs, it is shown that the interaction of a simulated alkaline sulphide-bearing submarine vent solution with a primeval anoxic iron-bearing ocean leads to the formation of chimney structures reminiscent of chemical gardens. These chimneys display periodicity in their deposition and exhibit diverse morphologies and mineralogies, affording the possibilities of catalysis and molecular sequestration. The addition of peptides and RNA to the alkaline solution modifies the elemental stoichiometry of the chimneys—perhaps indicating the very initial stage of the organic takeover on the way to living cells by charged organic polymers potentially synthesized in this same environment.
- Published
- 2012
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38. Affirmative Effects of Iloprost on Apoptosis during Ischemia–Reperfusion Injury in Kidney as a Distant Organ
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Arzu Kanik, Özden Vezir, Lokman Ayaz, Bahar Tunctan, Efsun S. Antmen, Barlas Aytacoglu, Oguz E. Gul, Seyhan Sahan-Firat, Necmiye Canacankatan, Belma Korkmaz, Nehir Sucu, Lülüfer Tamer, and Aysegul Gorur
- Subjects
Male ,Programmed cell death ,Ischemia ,Apoptosis ,Prostacyclin ,Pharmacology ,Kidney ,Critical Care and Intensive Care Medicine ,Nitric oxide ,chemistry.chemical_compound ,medicine ,Animals ,Iloprost ,Rats, Wistar ,business.industry ,General Medicine ,medicine.disease ,Rats ,medicine.anatomical_structure ,chemistry ,Nephrology ,Reperfusion Injury ,Anesthesia ,lipids (amino acids, peptides, and proteins) ,business ,Reperfusion injury ,medicine.drug - Abstract
Objective: Apoptosis and its regulatory mechanisms take part in renal ischemia–reperfusion (I/R) injury which can result in acute renal failure and the inhibition of the caspase is considered as a new therapeutic strategy. In this context, we investigated the antiapoptotic and cytoprotective effects of iloprost, a prostacyclin analog, in kidney as a distant organ. Methods: Wistar albino rats were randomized into five groups (n = 12 in each) as sham, ischemia, I/R, iloprost (10 µ gk g −1 ), and I/R + iloprost (10 µ gk g −1 ). A 4 h reperfusion procedure was carried out after 4 h of ischemia. Caspase-8 was evaluated for death receptor-induced pathways, whereas caspase-9 was evaluated for mitochondriadependent pathways and caspase-3 was investigated for overall apoptosis. Superoxide dismutase (SOD) enzyme activity and nitrite content as an indicator of nitric oxide (NO) production were also analyzed in kidney tissues. Results: Caspases-3, -8, and -9 were all significantly elevated in both ischemia and I/R groups compared to the sham group; however, treatment with iloprost reduced caspases-3, -8, and -9. SOD enzyme activity was attenuated by iloprost when compared to ischemic rats. The different effects of NO were found which change according to the present situation in ischemia, I/R, and treatment with iloprost. Conclusions: These findings suggested that iloprost prevents apoptosis in both receptor-induced and mitochondria-dependent pathways in renal I/R injury and it may be considered as a cytoprotective agent for apoptosis. Understanding the efficiency of iloprost on the pathways for cell death may lead to an opportunity in the therapeutic approach for renal I/R injury.
- Published
- 2011
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39. Characterization of Iron–Phosphate–Silicate Chemical Garden Structures
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Michael J. Russell, Isik Kanik, Galen D. Stucky, Lauren M. White, Ivria J. Doloboff, and Laura M. Barge
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Iron ,Silicates ,Inorganic chemistry ,Sodium silicate ,Surfaces and Interfaces ,Condensed Matter Physics ,Phosphate ,Chloride ,Silicate ,Phosphates ,chemistry.chemical_compound ,Hydrothermal Vents ,Membrane ,chemistry ,Potassium phosphate ,Electrochemistry ,medicine ,General Materials Science ,Ferrous Compounds ,Chemical garden ,Iron phosphate ,Spectroscopy ,medicine.drug - Abstract
Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life.
- Published
- 2011
- Full Text
- View/download PDF
40. Miniature mass spectrometer equipped with electrospray and desorption electrospray ionization for direct analysis of organics from solids and solutions
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Hugh I. Kim, Isik Kanik, R. Graham Cooks, Robert J. Noll, Luther W. Beegle, and Ewa Sokol
- Subjects
Electrospray ,Desorption electrospray ionization ,Chromatography ,Chemistry ,Electrospray ionization ,Analytical chemistry ,Miniature mass spectrometer ,Extractive electrospray ionization ,Condensed Matter Physics ,Mass spectrometry ,Tandem mass spectrometry ,Physical and Theoretical Chemistry ,Direct electron ionization liquid chromatography–mass spectrometry interface ,Instrumentation ,Spectroscopy - Abstract
We report on the use of a small light-weight mass spectrometer (MS) for chemical analysis of organic material directly from solution or from the solid state with potential value in future planetary missions. The mass spectrometer used in the experiments reported here is handheld and controlled from a laptop computer through custom software. Detection and identification of small organic molecules, including some that might be prebiotics, was achieved using methods relevant to in situ and remote sensing applications. The miniature MS was equipped with a discontinuous atmospheric pressure interface (DAPI) and a home-built electrosonic spray ionization (ESSI) source. Aqueous solutions of molecules of interest were examined using the ESSI technique, while desorption electrospray ionization (DESI) was applied to examine solid samples. The system performance was characterized by direct analysis of analytes belonging to several compound classes including biotic and abiotic amino acids, purines, pyrimidines, nucleosides and peptides. Detection limits in the sub-ppm range for solutions were achieved with the atmospheric pressure sampling/ionization interface. Tandem mass spectrometry (MS 2 ) was successfully applied to confirm trace detection of target compounds in mixtures. Multiple stage (MS n ) analysis, where n = 3–5, was employed for molecular structure confirmation and to demonstrate the high chemical specificity as well as the sensitivity of the instrumentation. The use of improved versions of this type of mass spectrometer on exploration missions could provide detailed chemical information on organic materials in physical states currently difficult to access. The high sensitivity and specificity, combined with rapid detection and the absence of requirements for sample preparation are encouraging features of the instrumentation.
- Published
- 2011
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- View/download PDF
41. Formation of radical species in photolyzed CH4:N2 ices
- Author
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Jay D. Goguen, Heather R. Howard, Paul V. Johnson, Robert Hodyss, and Isik Kanik
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Hydrogen ,Chemistry ,Radical ,Infrared spectroscopy ,chemistry.chemical_element ,Astronomy and Astrophysics ,medicine.disease_cause ,Photochemistry ,Dissociation (chemistry) ,Methane ,Astrobiology ,Pluto ,chemistry.chemical_compound ,Space and Planetary Science ,medicine ,Ultraviolet light ,Ultraviolet - Abstract
We report photochemical studies of thin cryogenic ice films composed of N 2 , CH 4 and CO in ratios analogous to those on the surfaces of Neptune’s largest satellite, Triton, and on Pluto. Experiments were performed using a hydrogen discharge lamp, which provides an intense source of ultraviolet light to simulate the sunlight-induced photochemistry on these icy bodies. Characterization via infrared spectroscopy showed that C 2 H 6 and C 2 H 2 , and HCO are formed by the dissociation of CH 4 into H, CH 2 and CH 3 and the subsequent reaction of these radicals within the ice. Other radical species, such as C 2 , C 2 - , CN, and CNN, are observed in the visible and ultraviolet regions of the spectrum. These species imply a rich chemistry based on formation of radicals from methane and their subsequent reaction with the N 2 matrix. We discuss the implications of the formation of these radicals for the chemical evolution of Triton and Pluto. Ultimately, this work suggests that C 2 - , CN, HCO, and CNN may be found in significant quantities on the surfaces of Triton and Pluto and that new observations of these objects in the appropriate wavelength regions are warranted.
- Published
- 2011
- Full Text
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42. Time Resolved Studies of Interfacial Reactions of Ozone with Pulmonary Phospholipid Surfactants Using Field Induced Droplet Ionization Mass Spectrometry
- Author
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Hugh I. Kim, Luther W. Beegle, Isik Kanik, Young Shik Shin, William A. Goddard, Hyungjun Kim, James R. Heath, and Jesse L. Beauchamp
- Subjects
Spectrometry, Mass, Electrospray Ionization ,Time Factors ,1,2-Dipalmitoylphosphatidylcholine ,Electrospray ionization ,Analytical chemistry ,Mass spectrometry ,Article ,Ion ,Surface-Active Agents ,chemistry.chemical_compound ,Ozone ,Pulmonary surfactant ,Ionization ,Monolayer ,Materials Chemistry ,Ozonide ,Physical and Theoretical Chemistry ,Phospholipids ,Ozonolysis ,Chemistry ,Air ,technology, industry, and agriculture ,Phosphatidylglycerols ,Pulmonary Surfactants ,Surfaces, Coatings and Films ,Phosphatidylcholines ,lipids (amino acids, peptides, and proteins) ,Oxidation-Reduction - Abstract
Field induced droplet ionization mass spectrometry (FIDI-MS) comprises a soft ionization method to sample ions from the surface of microliter droplets. A pulsed electric field stretches neutral droplets until they develop dual Taylor cones, emitting streams of positively and negatively charged submicrometer droplets in opposite directions, with the desired polarity being directed into a mass spectrometer for analysis. This methodology is employed to study the heterogeneous ozonolysis of 1-palmitoyl-2-oleoyl-sn-phosphatidylglycerol (POPG) at the air−liquid interface in negative ion mode using FIDI mass spectrometry. Our results demonstrate unique characteristics of the heterogeneous reactions at the air−liquid interface. We observe the hydroxyhydroperoxide and the secondary ozonide as major products of POPG ozonolysis in the FIDI-MS spectra. These products are metastable and difficult to observe in the bulk phase, using standard electrospray ionization (ESI) for mass spectrometric analysis. We also present studies of the heterogeneous ozonolysis of a mixture of saturated and unsaturated phospholipids at the air−liquid interface. A mixture of the saturated phospholipid 1,2-dipalmitoyl-sn-phosphatidylglycerol (DPPG) and unsaturated POPG is investigated in negative ion mode using FIDI-MS while a mixture of 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) and 1-stearoyl-2-oleoyl-sn-phosphatidylcholine (SOPC) surfactant is studied in positive ion mode. In both cases FIDI-MS shows the saturated and unsaturated pulmonary surfactants form a mixed interfacial layer. Only the unsaturated phospholipid reacts with ozone, forming products that are more hydrophilic than the saturated phospholipid. With extensive ozonolysis only the saturated phospholipid remains at the droplet surface. Combining these experimental observations with the results of computational analysis provides an improved understanding of the interfacial structure and chemistry of a surfactant layer system when subject to oxidative stress.
- Published
- 2010
- Full Text
- View/download PDF
43. Trace elements record depositional history of an Early Archean stromatolitic carbonate platform
- Author
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Abigail C. Allwood, Malcolm R. Walter, Ian W. Burch, Balz S. Kamber, and Isik Kanik
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biology ,Carbonate platform ,Pilbara Craton ,Archean ,Geochemistry ,Geology ,biology.organism_classification ,Sedimentary depositional environment ,chemistry.chemical_compound ,chemistry ,Stromatolite ,Geochemistry and Petrology ,Facies ,Carbonate ,Banded iron formation - Abstract
Rare earth elements and selected trace elements were measured in 48 samples of carbonate and chert from stromatolites and associated facies in the 3.45 billion year old Strelley Pool Formation, Pilbara Craton, Western Australia. The samples show coherent REE+Y patterns that vary systematically with sedimentary facies. Chert samples from bedded cherts beneath the Strelley Pool Formation and from the upper bedded chert members in the formation show REE+Y patterns consistent with originating by precipitation from hydrothermal and mixed marine-hydrothermal fluids. In contrast, carbonates and cherts from the stromatolitic reef member share the essential shale-normalized characteristics of other Archean marine precipitates (LREE depletion, positive La and Gd anomalies, absence of a negative Ce anomaly and a strongly superchondritic Y/Ho ratio). The close correspondence between REE+Y signatures and independent sedimentary facies interpretations is viewed as strong evidence for the primary nature of REE+Y patterns. They can thus be used as a proxy for the fluids from which sediments precipitated. Mixing hyperbolae can be constructed that reproduce the chemistry of cherts and carbonates by mixing of hydrothermal and marine fluid endmembers throughout the entire vertical succession from beneath the Strelley Pool Formation to the uppermost cherts. The mixing hyperbolae provide semi-quantitative confirmation that the trace element compositions across the suite of cherts represent different mixtures of ambient seawater and hydrothermal fluids. Our results indicate that the Earth's oldest supracrustal carbonates and associated cherts record important aspects of the REE geochemistry of the waters in which they precipitated, and provide valuable information on possible habitats of some of Earth's earliest biota.
- Published
- 2010
- Full Text
- View/download PDF
44. Modification of conductivity of P3HT by addition of endometallo fullerene
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N. K. Tripathi, Debmalya Roy, A. Saraiya, and Kanik Ram
- Subjects
Photoluminescence ,Fullerene ,Materials science ,Polymers and Plastics ,Analytical chemistry ,chemistry.chemical_element ,Heterojunction ,Germanium ,General Chemistry ,Atmospheric temperature range ,Conductivity ,Surfaces, Coatings and Films ,chemistry ,Electrical resistivity and conductivity ,Materials Chemistry ,Organic chemistry ,Graphite - Abstract
Germanium endometallo fullerene was syn- thesized by arcing Ge-impregnated graphite rod as anode and pure graphite rod as cathode. Photoluminescence (PL) and resistance measurements suggest that there are effec- tive interactions at the interface of Ge endometallo fullerene and poly 3-hexyl thiophene (P3HT). Four-fold enhancement of conductance has been found by adding just one weight percentage of Ge endometallo fullerene in the P3HT matrix at room temperature. However, at lower and higher tem- peratures, the enhancement in conductivity is low com- pared with room temperature, indicating the efficient charge transfer across the interface at the temperature range of 300-350 K. Atomic force microscopy (AFM) images also confirm the fact that temperature makes the more ordered heterojunctions between P3HT and Ge endohedral metallo- fullerene, which, in turn, trigger charge separation across interfaces. A sharp quenching in PL intensity of P3HT at room temperature by adding Ge endometallo fullerene indicates a strong interaction between the two and this composite material can be useful in photovoltaic cell. V C 2009
- Published
- 2009
- Full Text
- View/download PDF
45. HYDROGEN–DEUTERIUM EXCHANGE IN PHOTOLYZED METHANE–WATER ICES
- Author
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Amanda S. Weber, Robert Hodyss, Paul V. Johnson, Isik Kanik, and Karen Willacy
- Subjects
Physics ,Heavy water ,Astrochemistry ,Hydrogen ,Photodissociation ,chemistry.chemical_element ,Astronomy and Astrophysics ,medicine.disease_cause ,Photochemistry ,chemistry.chemical_compound ,chemistry ,Deuterium ,Space and Planetary Science ,medicine ,Ultraviolet light ,Hydrogen–deuterium exchange ,human activities ,Ultraviolet - Abstract
Previous work has concluded that H-D exchange occurs readily in polycyclic aromatic hydrocarbons frozen in deuterated water (D2O) irradiated with ultraviolet light. Here, we examine H-D exchange in methane-water ices following exposure to ultraviolet radiation and analyze the products formed as a result. We find that H-D exchange also occurs in methane-water ices by means of ultraviolet photolysis. Exchange proceeds through a radical mechanism that implies that almost all organic species will undergo significant H-D exchange with the matrix in water ices exposed to ultraviolet radiation. Given sufficient energetic processing of the ice, the H/D ratio of an ice matrix may be transferred to the organic species in the ice.
- Published
- 2009
- Full Text
- View/download PDF
46. Synthesis of germanium encapsulated fullerene
- Author
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N. K. Tripathi, Kanik Ram, Debmalya Roy, and Narayanasami Sathyamurthy
- Subjects
Fullerene ,Absorption spectroscopy ,Analytical chemistry ,General Chemistry ,Condensed Matter Physics ,chemistry.chemical_compound ,X-ray photoelectron spectroscopy ,chemistry ,Metallofullerene ,Physics::Atomic and Molecular Clusters ,Materials Chemistry ,Graphite ,Fourier transform infrared spectroscopy ,Inert gas ,Spectroscopy - Abstract
A method has been described for encapsulating Ge in a fullerene cage using GeO 2 and a graphite composite rod as anode and graphite as cathode. Annealing in an inert atmosphere before arcing, and the amount of GeO 2 in the rod determined the yield of Ge doped metallofullerene. Solvent extraction using soxlet in inert atmosphere followed by calcination in air was used to isolate metallofullerene from the soot. The insertion of Ge inside the fullerene was proven by ultra violet–visible absorption spectroscopy, matrix assisted laser desorption ionization-time of flight mass spectroscopy, Fourier transform infrared spectroscopy, energy-dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy.
- Published
- 2009
- Full Text
- View/download PDF
47. Photochemistry of methane–water ices
- Author
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Robert Hodyss, Isik Kanik, Julie V. Stern, Paul V. Johnson, and Jay D. Goguen
- Subjects
chemistry.chemical_compound ,Solar System ,chemistry ,Space and Planetary Science ,Radical ,Photodissociation ,Carbon dioxide ,Astronomy and Astrophysics ,Photochemistry ,Hydrogen peroxide ,Enceladus ,Methane ,Plume - Abstract
We report a study on the broadband ultraviolet photolysis of methane–water ice mixtures, at low methane concentrations and temperatures relevant to the icy satellites of the outer Solar System. The photochemistry of these mixtures is dominated by the action of hydroxyl radicals on methane and the resulting products. This implies that, given sufficient exposure time, the methane will eventually be completely oxidized to carbon dioxide. The presence of methane inhibits the formation of hydrogen peroxide by serving as a trap for hydroxyl radicals. The distribution of photochemical products is broadly similar to that previously conducted using ion and electron sources, with some differences possibly attributable to the difference in radiation source. The results are applicable to a variety of icy bodies in the Solar System. On Enceladus, where methane mixed with water is measured in the plumes, methane in the surface ices is subject to oxidation and will eventually be converted to CO 2 . The C H stretch feature detected in the VIMS spectra of the Enceladus surface ice suggests that methane is currently being supplied to the surface ice, likely from re-condensation of the plume gas.
- Published
- 2009
- Full Text
- View/download PDF
48. Magnetite nanoparticles by organic-phase synthetic route for carbon nanotube growth
- Author
-
Debmalya Roy and Kanik Ram
- Subjects
Materials science ,Hydrogen ,Nanoporous ,Mechanical Engineering ,Dispersity ,Metals and Alloys ,Nanoparticle ,chemistry.chemical_element ,Nanotechnology ,Carbon nanotube ,Condensed Matter Physics ,Microstructure ,Electronic, Optical and Magnetic Materials ,law.invention ,Chemical engineering ,chemistry ,Mechanics of Materials ,law ,Phase (matter) ,Materials Chemistry ,Powder diffraction - Abstract
In the present study, monodisperse Fe 3 O 4 nanoparticles with diameters ranging from 10 nm to 25 nm were synthesized using a simple organic-phase synthetic route and these monodispersed nanoparticles were then used as catalyst for seed growth of carbon nanotube. Fe 3 O 4 nanoparticles were reduced to iron nanoparticles assembly by Argon mixed with 5% Hydrogen gas at 400 °C and then it was examined by atomic force microscopy (AFM), thermomechanical analysis (TMA) and powder diffraction X-ray spectroscopic techniques. XRD indicates that iron clusters are bcc in nature and AFM image shows that the iron nanoparticles assemblies are 50–65 nm in size. To control the agglomeration of iron nanoparticles, nanoporous hybrid support material of Al 2 O 3 and SiO 2 was used. However, this matrix also fails to stop the agglomeration of iron nanoparticles mainly due to the inhomogeneous distribution of pore diameters. TMA analysis of iron clusters shows a temperature-dependent morphology, therefore, the CNTs growth temperature critically ascertain the nature and structure of CNTs.
- Published
- 2009
- Full Text
- View/download PDF
49. Electron impact dissociation of oxygen-containing molecules–A critical review
- Author
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Charles P. Malone, J. W. McConkey, Paul V. Johnson, Isik Kanik, C. Winstead, and Vincent McKoy
- Subjects
Physics ,General Physics and Astronomy ,chemistry.chemical_element ,Electron ,Oxygen ,Diatomic molecule ,Dissociation (chemistry) ,chemistry ,Chemical physics ,Ionization ,Molecule ,Atomic physics ,Excitation ,Electron ionization - Abstract
The dissociation of a wide range of oxygen-containing molecules following impact with electrons of carefully controlled energy is critically reviewed. Molecules considered range from diatomics, like O_2 and CO, to large molecules of biological and technological interest. Dissociation mechanisms are discussed and, where possible, quantitative data for the various possible processes, ionization, attachment, dissociation, excitation, emission etc., are presented. Gaps and discrepancies in our current data base are highlighted. Both graphical and tabular data are presented.
- Published
- 2008
- Full Text
- View/download PDF
50. Textural and mineralogical biosignatures in an unusual microbialite from Death Valley, California
- Author
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Susanne Douglas, Pamela G. Conrad, Isik Kanik, William Abbey, and Randall E. Mielke
- Subjects
Calcite ,Gypsum ,Mineral ,Geochemistry ,Astronomy and Astrophysics ,Context (language use) ,Mars Exploration Program ,engineering.material ,Texture (geology) ,Abiogenic petroleum origin ,chemistry.chemical_compound ,chemistry ,Space and Planetary Science ,Biosignature ,engineering ,Geology - Abstract
For in situ astrobiological studies of Mars or other planets, we must employ strategies that will enable us to verify whether our approach and prototype instruments are actually capable of distinguishing life from non-life. This must be done against a background of rigorously conducted scientific characterization of the environment or sample types being considered for measurement by the instruments under development. In this study we show how a combination of mineralogical and textural features can be considered a biosignature in an early Mars analogue environment, Death Valley, California. We propose that it is a combination of features in context of the geologic matrix which allows determination of biogenicity to be made. Polymineralic microbialites (organosedimentary formations constructed by microorganisms) from a spring pool at Badwater, within Death Valley National Park, are composed of alternating biogenic and abiogenic minerals in a distinct triplet sequence related to wet and dry seasons. A microbial community, occurring as a black biofilm, produced paired layers of two different mineral types: manganese oxyhydroxides and calcite. These biogenic layers are separated from the next pair by a gypsum layer and appear to be laid down in the wet season, with the gypsum (a mineral positively identified on Mars) precipitating in the dry part of the year, abiogenically (i.e., not dependent on microbial metabolic activity for its deposition). In addition, textural features (smaller grain size and less geometric morphology) unique to the biogenic vs the abiogenic layers, were consistently observed so that texture served as a biosignature in this environment.
- Published
- 2008
- Full Text
- View/download PDF
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