Search results for: Atoms in molecules

Authors: Amid Ranjkesh, Milan Ambrožič, Samo Kralj

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We study the typical domain size and configuration character of a randomly perturbed system exhibiting continuous symmetry breaking. As a model system we use rod-like objects within a cubic lattice interacting via a Lebwohl–Lasher-type interaction. We describe their local direction with a headless unit director field. An example of such systems represents nematic LC or nanotubes. We further introduce impurities of concentration p, which impose the random anisotropy field-type disorder to directors. We study the domain-type pattern of molecules as a function of p, anchoring strength w between a neighboring director and impurity, temperature, history of samples. In simulations we quenched the directors either from the random or homogeneous initial configuration. Our results show that a history of system strongly influences: i) the average domain coherence length; and ii) the range of ordering in the system. In the random case the obtained order is always short ranged (SR). On the contrary, in the homogeneous case, SR is obtained only for strong enough anchoring and large enough concentration p. In other cases, the ordering is either of quasi long range (QLR) or of long range (LR). We further studied memory effects for the random initial configuration. With increasing external ordering field B either QLR or LR is realized.

Keywords: Lebwohl-Lasher model, liquid crystals, disorder, memory effect, orientational order.

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Authors: Soukaina Motia, Nadia El Alami El Hassani, Alassane Diouf, Benachir Bouchikhi, Nezha El Bari

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Parabens are the antimicrobial molecules largely used in cosmetic products as a preservative agent. Among them, the methylparaben (MP) is the most frequently used ingredient in cosmetic preparations. Nevertheless, their potential dangers led to the development of sensible and reliable methods for their determination in environmental samples. Firstly, a sensitive and selective molecular imprinted polymer (MIP) based on screen-printed gold electrode (Au-SPE), assembled on a polymeric layer of carboxylated poly(vinyl-chloride) (PVC-COOH), was developed. After the template removal, the obtained material was able to rebind MP and discriminate it among other interfering species such as glucose, sucrose, and citric acid. The behavior of molecular imprinted sensor was characterized by Cyclic Voltammetry (CV), Differential Pulse Voltammetry (DPV) and Electrochemical Impedance Spectroscopy (EIS) techniques. Then, the biosensor was found to have a linear detection range from 0.1 pg.mL^-1 to 1 ng.mL^-1 and a low limit of detection of 0.12 fg.mL^-1 and 5.18 pg.mL^-1 by DPV and EIS, respectively. For applications, this biosensor was employed to determine MP content in four wastewaters in Meknes city and two cosmetic products (shower gel and shampoo). The operational reproducibility and stability of this biosensor were also studied. Secondly, another MIP biosensor based on tungsten trioxide (WO₃) functionalized by gold nanoparticles (Au-NPs) assembled on a polymeric layer of PVC-COOH was developed. The main goal was to increase the sensitivity of the biosensor. The developed MIP biosensor was successfully applied for the MP determination in wastewater samples and cosmetic products.

Keywords: Cosmetic products, methylparaben, molecularly imprinted polymer, wastewater.

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Authors: Wenjun Zhang, Yunqing Du, Ming L. Wang

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Noninvasive diagnostics of diseases via breath analysis has attracted considerable scientific and clinical interest for many years and become more and more promising with the rapid advancements in nanotechnology and biotechnology. The volatile organic compounds (VOCs) in exhaled breath, which are mainly blood borne, particularly provide highly valuable information about individuals’ physiological and pathophysiological conditions. Additionally, breath analysis is noninvasive, real-time, painless, and agreeable to patients. We have developed a wireless sensor array based on single-stranded DNA (ssDNA)-functionalized single-walled carbon nanotubes (SWNT) for the detection of a number of physiological indicators in breath. Seven DNA sequences were used to functionalize SWNT sensors to detect trace amount of methanol, benzene, dimethyl sulfide, hydrogen sulfide, acetone, and ethanol, which are indicators of heavy smoking, excessive drinking, and diseases such as lung cancer, breast cancer, and diabetes. Our test results indicated that DNA functionalized SWNT sensors exhibit great selectivity, sensitivity, and repeatability; and different molecules can be distinguished through pattern recognition enabled by this sensor array. Furthermore, the experimental sensing results are consistent with the Molecular Dynamics simulated ssDNAmolecular target interaction rankings. Thus, the DNA-SWNT sensor array has great potential to be applied in chemical or biomolecular detection for the noninvasive diagnostics of diseases and personal health monitoring.

Keywords: Breath analysis, DNA-SWNT sensor array, diagnosis, noninvasive.

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Authors: Dionisios Panagiotaras, Elias Stathatos, Dimitrios Papoulis

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 Sol-gel method has been used to fabricate nanocomposite films on glass substrates composed halloysite clay mineral and nanocrystalline TiO2. The methodology for the synthesis involves a simple chemistry method utilized nonionic surfactant molecule as pore directing agent along with the acetic acid-based solgel route with the absence of water molecules. The thermal treatment of composite films at 450oC ensures elimination of organic material and lead to the formation of TiO2 nanoparticles onto the surface of the halloysite nanotubes. Microscopy techniques and porosimetry methods used in order to delineate the structural characteristics of the materials. The nanocomposite films produced have no cracks and active anatase crystal phase with small crystallite size were deposited on halloysite nanotubes. The photocatalytic properties for the new materials were examined for the decomposition of the Basic Blue 41 azo dye in solution. These, nanotechnology based composite films show high efficiency for dye’s discoloration in spite of different halloysite quantities and small amount of halloysite/TiO2 catalyst immobilized onto glass substrates. Moreover, we examined the modification of the halloysite/TiO2 films with silver particles in order to improve the photocatalytic properties of the films. Indeed, the presence of silver nanoparticles enhances the discoloration rate of the Basic Blue 41 compared to the efficiencies obtained for unmodified films.

Keywords: Clay mineral, nanotubular Halloysite, Photocatalysis, Titanium Dioxide, Silver modification.

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Authors: Olusola Olalekan Elekofehinti, Isaac Gbadura Adanlawo, Joao Batista Teixeira Rocha

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The potential neuroprotective effect of Phyllantus nuriri against Fe2+ and sodium nitroprusside (SNP) induced oxidative stress in mitochondria of rats brain was evaluated. Cellular viability was assessed by MTT reduction, reactive oxygen species (ROS) generation was measured using the probe 2,7-dichlorofluoresce indiacetate (DCFH-DA). Glutathione content was measured using dithionitrobenzoic acid (DTNB). Fe2+ (10μM) and SNP (5μM) significantly decreased mitochondrial activity, assessed by MTT reduction assay, in a dose-dependent manner, this occurred in parallel with increased glutathione oxidation, ROS production and lipid peroxidation end-products (thiobarbituric acid reactive substances, TBARS). The co-incubation with methanolic extract of Phyllantus nuriri (10-200 μg/ml) reduced the disruption of mitochondrial activity, gluthathione oxidation, ROS production as well as the increase in TBARS levels caused by both Fe2+ and SNP in a dose dependent manner. HPLC analysis of the extract revealed the presence of gallic acid (20.540.01), caffeic acid (7.930.02), rutin (25.310.05), quercetin (31.280.03) and kaemferol (14.360.01). This result suggests that these phytochemicals account for the protective actions of P. niruri against Fe2+ and SNP -induced oxidative stress. Our results show that P. nuriri consist important bioactive molecules in the search for an improved therapy against the deleterious effects of Fe2+, an intrinsic producer of reactive oxygen species (ROS), that leads to neuronal oxidative stress and neurodegeneration.

Keywords: Phyllantus niruri, mitochondria, antioxidant, oxidative stress, synaptosome.

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Authors: Jing Zhang, Lian Wu, Jie-ming Qu, Chun-xue Bai, Mervyn J Merrilees, Peter N Black

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COPD is characterized by loss of elastic fibers from small airways and alveolar walls, with the decrease in elastin increasing with disease severity. It is unclear why there is a lack of repair of elastic fibers. We have examined fibroblasts cultured from lung tissue from normal and COPD subjects to determine if the secretory profile explains lack of tissue repair. In this study, fibroblasts were cultured from lung parenchyma of bronchial carcinoma patients with varying degrees of COPD; controls (non-COPD, n=5), mild COPD (GOLD 1, n=5) and moderate-severe COPD (GOLD 2-3, n=12). Measurements were made of proliferation, senescence-associated beta-galactosidase-1, mRNA expression of IL-6, IL-8, MMP-1, tropoelastin and versican, and protein levels for IL-6, IL-8, PGE2, tropoelastin, insoluble elastin, and versican. It was found that GOLD 2-3 fibroblasts proliferated more slowly (p<0.01) and had higher levels of senescence-associated beta-galactosidase-1 (p<0.001) than controls (non-COPD). GOLD 2-3 fibroblasts showed significant increases in mRNA and/or protein for IL-6, IL-8, MMP-1, PGE2, versican (p<0.01) and tropoelastin (p<0.05). mRNA expression and/or protein levels of tropoelastin (p<0.01), versican (p<0.02), IL-6 (p<0.05) and IL-8 (p<0.05) were negatively correlated with FEV1%. Insoluble elastin was not increased. In summary, fibroblasts from moderate to severe COPD subjects display a secretory phenotype with up-regulation of inflammatory molecules including the matrix proteoglycan versican, and increased soluble, but not insoluble, elastin. Versican inhibits assembly of tropoelastin into insoluble elastin and we conclude that the pro-inflammatory phenotype of COPD fibroblasts it is not compatible with repair elastic fibers.

Keywords: COPD, pulmonary fibroblasts, pro-inflammatory phenotype, versican, elastin

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Authors: Surender Singh Jadav, Venkatesan Jayaprakash, Arijit Basu, Barij Nayan Sinha

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Chikungunya virus (CHICKV) is an arboviruses belonging to family Tagoviridae and is transmitted to human through by mosquito (Aedes aegypti and Aedes albopictus) bite. A large outbreak of chikungunya has been reported in India between 2006 and 2007, along with several other countries from South-East Asia and for the first time in Europe. It was for the first time that the CHICKV outbreak has been reported with mortality from Reunion Island and increased mortality from Asian countries. CHICKV affects all age groups, and currently there are no specific drugs or vaccine to cure the disease. The need of antiviral agents for the treatment of CHICKV infection and the success of virtual screening against many therapeutically valuable targets led us to carry out the structure based drug design against Chikungunya nSP2 protease (PDB: 3TRK). Highthroughput virtual screening of publicly available databases, ZINC12 and BindingDB, has been carried out using the Openeye tools and Schrodinger LLC software packages. Openeye Filter program has been used to filter the database and the filtered outputs were docked using HTVS protocol implemented in GLIDE package of Schrodinger LLC. The top HITS were further used for enriching the similar molecules from the database through vROCS; a shape based screening protocol implemented in Openeye. The approach adopted has provided different scaffolds as HITS against CHICKV protease. Three scaffolds: Indole, Pyrazole and Sulphone derivatives were selected based on the docking score and synthetic feasibility. Derivatives of Pyrazole were synthesized and submitted for antiviral screening against CHICKV.

Keywords: Chikungunya, nsP2 protease, ADME filter, HTVS, Docking, Active site.

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Authors: Mustafa M. Donma, Sule G. Kacmaz, Ahsen Yilmaz, Savas Guzel, Orkide Donma

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Obesity, as excessive fat accumulation in the body, is a global health problem. The prevalence of obesity and its complications increase due to easy access to high-energy food and decreased physical activity. Cardiovascular diseases (CVDs) constitute a significant part of obesity-related morbidity and mortality. Since the effects of obesity on cardiovascular system may start during childhood without clinical findings, elucidating the mechanisms of cardiovascular changes associated with childhood obesity became more important. In this study, we aimed to investigate some biochemical parameters which may be involved in obesity-related pathologic processes of CVDs. One hundred and seventy-seven children were included in the study, and they were divided into four groups based upon WHO criteria and presence of the metabolic syndrome (MetS): children with normal-BMI, obesity, morbid obesity, and MetS. High-sensitive cardiac troponin T (hs-cTnT), cardiac myosin binding protein C (cMyBP-C), trimethylamine N-oxide (TMAO), soluble tumor necrosis factor-like weak inducer (sTWEAK), chromogranin A (CgA), multimerin-2 levels, and other biochemical parameters were measured in serum samples. Anthropometric measurements and clinical findings of the children were recorded. Statistical analyses were performed. Children with normal-BMI had significantly higher CgA levels than children with obesity, morbid obesity, and MetS (p < 0.05). Cardiac MyBP-C levels of children with MetS were significantly higher than of children with normal-BMI and OB children (p < 0.05). There was no significant difference in hs-cTnT, sTWEAK, TMAO and multimerin-2 between the groups (p>0.05). These results suggested that cMyBP-C and CgA molecules may be involved in the pathogenesis of obesity-related CVDs.

Keywords: biomarker, cardiovascular diseases, children, obesity

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Authors: Ching-Wei Tsai, Chih-I Liu, Ruoh-Chyu Ruaana

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A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.

Keywords: Protein Oriented immobilization, Molecular docking, ligand design, surface modification.

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Authors: Md. Z. Alam, Amal A. Elgharbawy, Muhammad Moniruzzaman, Nassereldeen A. Kabbashi, Parveen Jamal

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The enzymatic hydrolysis of lignocellulosic biomass is one of the obstacles in the process of sugar production, due to the presence of lignin that protects the cellulose molecules against cellulases. Although the pretreatment of lignocellulose in ionic liquid (IL) system has been receiving a lot of interest; however, it requires IL removal with an anti-solvent in order to proceed with the enzymatic hydrolysis. At this point, introducing a compatible cellulase enzyme seems more efficient in this process. A cellulase enzyme that was produced by Trichoderma reesei on palm kernel cake (PKC) exhibited a promising stability in several ILs. The enzyme called PKC-Cel was tested for its optimum pH and temperature as well as its molecular weight. One among evaluated ILs, 1,3-diethylimidazolium dimethyl phosphate [DEMIM] DMP was applied in this study. Evaluation of six factors was executed in Stat-Ease Design Expert V.9, definitive screening design, which are IL/ buffer ratio, temperature, hydrolysis retention time, biomass loading, cellulase loading and empty fruit bunches (EFB) particle size. According to the obtained data, IL-enzyme system shows the highest sugar concentration at 70 °C, 27 hours, 10% IL-buffer, 35% biomass loading, 60 Units/g cellulase and 200 μm particle size. As concluded from the obtained data, not only the PKC-Cel was stable in the presence of the IL, also it was actually stable at a higher temperature than its optimum one. The reducing sugar obtained was 53.468±4.58 g/L which was equivalent to 0.3055 g reducing sugar/g EFB. This approach opens an insight for more studies in order to understand the actual effect of ILs on cellulases and their interactions in the aqueous system. It could also benefit in an efficient production of bioethanol from lignocellulosic biomass.

Keywords: Cellulase, hydrolysis, lignocellulose, pretreatment, stability.

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Authors: A. Alzeyadi, E. Loffill, R. Alkhaddar

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Continuous upflow filters can combine the nutrient (nitrogen and phosphate) and suspended solid removal in one unit process. The contaminant removal could be achieved chemically or biologically; in both processes the filter removal efficiency depends on the interaction between the packed filter media and the influent. In this paper a residence time distribution (RTD) study was carried out to understand and compare the transfer behaviour of contaminants through a selected filter media packed in a laboratory-scale continuous up flow filter; the selected filter media are limestone and white dolomite. The experimental work was conducted by injecting a tracer (red drain dye tracer –RDD) into the filtration system and then measuring the tracer concentration at the outflow as a function of time; the tracer injection was applied at hydraulic loading rates (HLRs) (3.8 to 15.2 m h-1). The results were analysed according to the cumulative distribution function F(t) to estimate the residence time of the tracer molecules inside the filter media. The mean residence time (MRT) and variance σ2 are two moments of RTD that were calculated to compare the RTD characteristics of limestone with white dolomite. The results showed that the exit-age distribution of the tracer looks better at HLRs (3.8 to 7.6 m h-1) and (3.8 m h-1) for limestone and white dolomite respectively. At these HLRs the cumulative distribution function F(t) revealed that the residence time of the tracer inside the limestone was longer than in the white dolomite; whereas all the tracer took 8 minutes to leave the white dolomite at 3.8 m h-1. On the other hand, the same amount of the tracer took 10 minutes to leave the limestone at the same HLR. In conclusion, the determination of the optimal level of hydraulic loading rate, which achieved the better influent distribution over the filtration system, helps to identify the applicability of the material as filter media. Further work will be applied to examine the efficiency of the limestone and white dolomite for phosphate removal by pumping a phosphate solution into the filter at HLRs (3.8 to 7.6 m h-1).

Keywords: Filter media, hydraulic loading rate, residence time distribution, tracer.

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Authors: Makhlouf Mourad, Messabih Sidi Mohamed, Bouchher Omar, Houali Farida, Benrachedi Khaled

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Mesoporous materials are very commonly used as adsorbent materials for removing phenolic compounds. However, the adsorption mechanism of these compounds is still poorly controlled. However, understanding the interactions mesoporous materials/adsorbed molecules is very important in order to optimize the processes of liquid phase adsorption. The difficulty of synthesis is to keep an orderly and cubic pore structure and achieve a homogeneous surface modification. The grafting of Si(CH₃)₃ was chosen, to transform hydrophilic surfaces hydrophobic surfaces. The aim of this work is to study the kinetics and thermodynamics of two volatile organic compounds VOC phenol (PhOH) and P hydroxy benzoic acid (4AHB) on a mesoporous material of type MCM-48 grafted with an organosilane of the Trimethylchlorosilane (TMCS) type, the material thus grafted or functionalized (hereinafter referred to as MCM-48-G). In a first step, the kinetic and thermodynamic study of the adsorption isotherms of each of the VOCs in mono-solution was carried out. In a second step, a similar study was carried out on a mixture of these two compounds. Kinetic models (pseudo-first order, pseudo-second order) were used to determine kinetic adsorption parameters. The thermodynamic parameters of the adsorption isotherms were determined by the adsorption models (Langmuir, Freundlich). The comparative study of adsorption of PhOH and 4AHB proved that MCM-48-G had a high adsorption capacity for PhOH and 4AHB; this may be related to the hydrophobicity created by the organic function of TMCS in MCM-48-G. The adsorption results for the two compounds using the Freundlich and Langmuir models show that the adsorption of 4AHB was higher than PhOH. The values ​​obtained by the adsorption thermodynamics show that the adsorption interactions for our sample with the phenol and 4AHB are of a physical nature. The adsorption of our VOCs on the MCM-48 (G) is a spontaneous and exothermic process.

Keywords: Adsorption, kinetics, isotherm, mesoporous materials, TMCS, phenol, P-hydroxy benzoic acid.

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Authors: Srinivas Bathini, Duraichelvan Raju, Simona Badilescu, Muthukumaran Packirisamy

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A bio-sensing method, based on the plasmonic property of gold nano-islands, has been developed for detection of exosomes in a clinical setting. The position of the gold plasmon band in the UV-Visible spectrum depends on the size and shape of gold nanoparticles as well as on the surrounding environment. By adsorbing various chemical entities, or binding them, the gold plasmon band will shift toward longer wavelengths and the shift is proportional to the concentration. Exosomes transport cargoes of molecules and genetic materials to proximal and distal cells. Presently, the standard method for their isolation and quantification from body fluids is by ultracentrifugation, not a practical method to be implemented in a clinical setting. Thus, a versatile and cutting-edge platform is required to selectively detect and isolate exosomes for further analysis at clinical level. The new sensing protocol, instead of antibodies, makes use of a specially synthesized polypeptide (Vn96), to capture and quantify the exosomes from different media, by binding the heat shock proteins from exosomes. The protocol has been established and optimized by using a glass substrate, in order to facilitate the next stage, namely the transfer of the protocol to a microfluidic environment. After each step of the protocol, the UV-Vis spectrum was recorded and the position of gold Localized Surface Plasmon Resonance (LSPR) band was measured. The sensing process was modelled, taking into account the characteristics of the nano-island structure, prepared by thermal convection and annealing. The optimal molar ratios of the most important chemical entities, involved in the detection of exosomes were calculated as well. Indeed, it was found that the results of the sensing process depend on the two major steps: the molar ratios of streptavidin to biotin-PEG-Vn96 and, the final step, the capture of exosomes by the biotin-PEG-Vn96 complex. The microfluidic device designed for sensing of exosomes consists of a glass substrate, sealed by a PDMS layer that contains the channel and a collecting chamber. In the device, the solutions of linker, cross-linker, etc., are pumped over the gold nano-islands and an Ocean Optics spectrometer is used to measure the position of the Au plasmon band at each step of the sensing. The experiments have shown that the shift of the Au LSPR band is proportional to the concentration of exosomes and, thereby, exosomes can be accurately quantified. An important advantage of the method is the ability to discriminate between exosomes having different origins.

Keywords: Exosomes, gold nano-islands, microfluidics, plasmonic biosensing.

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Authors: U. K. Sahin, N. Erdumlu, C. Saricam, I. Gocek, M. H. Arslan, H. Acikgoz-Tufan, B. Kalav

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Finishing is an important part of fabric processing with which a wide range of features are imparted to greige or colored fabrics for various end-uses. Especially, by the addition or impartation of nano-scaled particles to the fabric structure composite fabrics, a kind of composite materials can be acquired. Composite materials, generally shortened as composites or in other words composition materials, are engineered or naturally occurring materials made from two or more component materials with significantly different physical, mechanical or chemical characteristics remaining separate and distinctive at the macroscopic or microscopic scale within the end product structure. Therefore, the technique finishing which is one of the fundamental methods to be applied on fabrics for obtainment of composite fabrics with many functionalities was used in the current study with the same purpose. However, regardless of the finishing materials applied, the efficient life of finished product on offering desired feature is low, since the durability of finishes on the material is limited. Any increase in durability of these finishes on textiles would enhance the life of use for textiles, which will result in happier users. Therefore, in this study, since higher durability was desired for the finishing materials fixed on the fabrics, nano-scaled hollow structured cyclodextrins were chemically imparted by grafting to the structure of conventional cotton fabrics by the help of finishing technique in order to be fixed permanently. By this way, a processed and functionalized base fabric having potential to be treated in the subsequent processes with many different finishing agents and nanomaterials could be obtained. Henceforth, this fabric can be used as a multi-functional fabric due to the encapturing ability of cyclodextrins to molecules/particles via physical/chemical means. In this study, scoured and rinsed woven bleached plain weave 100% cotton fabrics were utilized because textiles made of cotton are the most demanded textile products in the textile market by the textile consumers in daily life. Cotton fabric samples were immersed in treating baths containing β-cyclodextrin and 1,2,3,4-butanetetracarboxylic acid and to reduce the curing temperature the catalyst sodium hypophosphite monohydrate was used. All impregnated fabric samples were pre-dried. The reaction of grafting was performed in dry state. The treated and cured fabric samples were rinsed with warm distilled water and dried. The samples were dried for 4 h and weighed before and after finishing and rinsing. Stability and durability of β-cyclodextrins on fabric surface against external factors such as washing as well as strength of functionalized fabric in terms of tensile and tear strength were tested. Presence and homogeneity of distribution of β-cyclodextrins on fabric surface were characterized.

Keywords: Cotton fabric, cyclodextrin, improved durability, multifunctional composite textile.

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