Search results for: laboratory molecular diagnostics

Authors: Reema K. AlEssa, Sahar Alshomer, Abdullah Alfaleh, Sultan ALkhenaizan, Mohammed Albalwi

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Ichthyosis is a disorder of abnormal keratinization, characterized by excessive scaling, and consists of more than twenty subtypes varied in severity, mode of inheritance, and the genes involved. There is insufficient data in the literature about the epidemiology and characteristics of ichthyosis locally. Our aim is to identify the histopathological features and genetic profile of ichthyosis. Method: It is an observational retrospective case series study conducted in March 2020, included all patients who were diagnosed with Ichthyosis and confirmed by histological and molecular findings over the last 20 years in King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia. Molecular analysis was performed by testing genomic DNA and checking genetic variations using the AmpliSeq panel. All disease-causing variants were checked against HGMD, ClinVar, Genome Aggregation Database (gnomAD), and Exome Aggregation Consortium (ExAC) databases. Result: A total of 60 cases of Ichthyosis were identified with a mean age of 13 ± 9.2. There is an almost equal distribution between female patients 29 (48%) and males 31 (52%). The majority of them were Saudis, 94%. More than half of patients presented with general scaling 33 (55%), followed by dryness and coarse skin 19 (31.6%) and hyperlinearity 5 (8.33%). Family history and history of consanguinity were seen in 26 (43.3% ), 13 (22%), respectively. History of colloidal babies was found in 6 (10%) cases of ichthyosis. The most frequent genes were ALOX12B, ALOXE3, CERS3, CYP4F22, DOLK, FLG2, GJB2, PNPLA1, SLC27A4, SPINK5, STS, SUMF1, TGM1, TGM5, VPS33B. Most frequent variations were detected in CYP4F22 in 16 cases (26.6%) followed by ALOXE3 6 (10%) and STS 6 (10%) then TGM1 5 (8.3) and ALOX12B 5 (8.3). The analysis of molecular genetic identified 23 different genetic variations in the genes of ichthyosis, of which 13 were novel mutations. Homozygous mutations were detected in the majority of ichthyosis cases, 54 (90%), and only 1 case was heterozygous. Few cases, 4 (6.6%) had an unknown type of ichthyosis with a negative genetic result. Conclusion: 13 novel mutations were discovered. Also, about half of ichthyosis patients had a positive history of consanguinity.

Keywords: ichthyosis, genetic profile, molecular characterization, congenital ichthyosis

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Authors: Sylwia Baluta, Joanna Cabaj, Karol Malecha

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The evolution of biosensors was driven by the need for faster and more versatile analytical methods for application in important areas including clinical, diagnostics, food analysis or environmental monitoring, with minimum sample pretreatment. Rapid and sensitive neurotransmitters detection is extremely important in modern medicine. These compounds mainly occur in the brain and central nervous system of mammals. Any changes in the neurotransmitters concentration may lead to many diseases, such as Parkinson’s or schizophrenia. Classical techniques of chemical analysis, despite many advantages, do not permit to obtain immediate results or automatization of measurements.

Keywords: adrenaline, biosensor, dopamine, laccase, tyrosinase

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Authors: M. M. Mekkakia, M. P Luong, A. Arab

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These controlling the water content of compaction are a major concern of fundamental civil engineers. Also, the knowledge of the fundamentals of the behaviour of compacted clay soils is essential to predict and quantify the effects of a change in water content. The study of unsaturated soils is a very complex area which several studies are directed to in recent years. Our job work is to perform tests of Proctor, Oedometer and shear, on samples of unsaturated clay in order to see the influence of water content on the compressibility and the shear strength. The samples were prepared at different amounts of water from water content to optimum water contents close to saturation. This study thus allowed us to measure and monitor the parameters of compressibility and shear strength as a function of water content.

Keywords: laboratory tests, clay, unsaturated soil, atterberg limits, compaction, compressibility, shear

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Authors: Amanda M. Tadini, Houssam Hajjoul, Gustavo Nicolodelli, Stéphane Mounier, Célia R. Montes, Débora M. B. P. Milori

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Soil organic matter (SOM) plays an important role in maintaining soil productivity and accounting for the promotion of biological diversity. The main components of the SOM are the humic substances which can be fractionated according to its solubility in humic acid (HA), fulvic acids (FA) and humin (HU). The determination of the chemical properties of organic matter as well as its interaction with metallic species is an important tool for understanding the structure of the humic fractions. Fluorescence spectroscopy has been studied as a source of information about what is happening at the molecular level in these compounds. Specially, soils of Amazon region are an important ecosystem of the planet. The aim of this study is to understand the molecular and structural composition of HA samples from Spodosol of Amazonia using the fluorescence Emission-Excitation Matrix (EEM) and Time Resolved Fluorescence Spectroscopy (TRFS). The results showed that the samples of HA showed two fluorescent components; one has a more complex structure and the other one has a simpler structure, which was also seen in TRFS through the evaluation of each sample lifetime. Thus, studies of this nature become important because it aims to evaluate the molecular and structural characteristics of the humic fractions in the region that is considered as one of the most important regions in the world, the Amazon.

Keywords: Amazonian soil, characterization, fluorescence, humic acid, lifetime

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Authors: Desouky Abd El Haleem, Sahar Zaki

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This work was conducted to develop a one-step multiplex PCR system for rapid, sensitive, and specific detection of three different bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, and Salmonella spp, directly in wastewater without prior isolation on selective media. As a molecular confirmatory test after isolation of the pathogens by classical microbiological methods, PCR-RFLP of their amplified 16S rDNA genes was performed. It was observed that the developed protocols have significance impact in the ability to detect sensitively, rapidly and specifically the three pathogens directly in water within short-time, represents a considerable advancement over more time-consuming and less-sensitive methods for identification and characterization of these kinds of pathogens.

Keywords: multiplex PCR, bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, Salmonella spp.

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Determination of the behavior of clathrate hydrate with inhibitor in the THz region will provide useful information about hydrate plug control in the upstream of the oil and gas industry. In this study, terahertz time-domain spectroscopy (THz-TDS) revealed the inhibition of the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different molecular weights. Distinct footprints of phase transition in the THz region (0.4–2.2 THz) were analyzed and absorption coefficients and real part of refractive indices are obtained in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz spectroscopy, tetrahydrofuran, inhibitor

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Authors: Seyedmajid Mehrnia, Maximilan Kuhr, Peter F. Pelz

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Molecular Dynamics (MD) simulation is a proven method to inspect behaviours of lubricant oils in nano-scale gaps. However, most MD simulations on tribology have been performed with atomically smooth walls to determine wall slip and friction properties. This study will investigate the effect of porosity, specifically nano-porous walls, on wall slip properties of hydrocarbon oils confined between two walls in a Couette flow. Different pore geometries will be modelled to investigate the effect on wall slip and bulk shear. In this paper, the Polyalphaolefin (PAO) molecules are confined to a stationary and a moving wall. A hybrid force field consisting of different potential energy functions was employed in this MD simulation. Newton’s law defines how those forces will influence the atoms' movements. The interactions among surface atoms were simulated with an Embedded Atom Method (EAM) potential function which can represent the characteristics of metallic arrangements very strongly. We implemented NERD forcefield for intramolecular potential energy function. Also, Lennard-Jones potential was employed for nonbonded intermolecular interaction.

Keywords: slip length, molecular dynamics, critical shear rate, Couette flow

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Authors: Umar Adli Amran, Tan Choon Chek, Mohd Shahkhirat Norizan, Then Kek Hoe

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Controlled release fertilizer (CRF) enables a regulated nutrients release for more efficient plant uptake compared to the normal granular fertilizer. It reduces nutrients loss via surface run-off and leaching, hence promotes sustainable agriculture. Although the performance of CRF in providing consistent and timely nutrients supply is well known, its expensive price limits it usage in a large scale plantation. This study is conducted to evaluate the properties and performance of bio-based polyurethane (PU)-coated CRF via laboratory and oil palm main nursery trial. The CRF is produced by coating of a normal commercial compound granular fertilizer from FGV Fertiliser Sdn. Bhd., namely Felda 10 (10.5-8-20-3+0.5B), and designated as CRF FGV10. Based on laboratory evaluation, the CRF FGV10 can sustain nutrients release for more than 6 months. Vegetative growth parameters such as girth size, palm height, third frond length, and the total number of fronds produced were recorded. Besides that, dry biomass of the oil palm seedlings was also determined. From the evaluation, it is proved that at 50% reduction of nutrients application rate and for only two times application (T3), CRF FGV10 enabled the oil palm seedlings to achieve similar vegetative growth with the control samples (T1). It is also proven that only PU-coated CRF FGV10 had allowed the reduction of fertilizer rate and application rounds.

Keywords: nutrition, oil palm seedlings, polyurethane, sustainable manuring, vegetative growth

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Authors: Syed Asif Hassan, Syed Atif Hassan

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Multidrug-resistant Tuberculosis (MDR-TB) is an infection caused by the resistant strains of Mycobacterium tuberculosis that do not respond either to isoniazid or rifampicin, which are the most important anti-TB drugs. The increase in the occurrence of a drug-resistance strain of MTB calls for an intensive search of novel target-based therapeutics. In this context LprG (Rv1411c) a lipoprotein from MTB plays a pivotal role in the immune evasion of Mtb leading to survival and propagation of the bacterium within the host cell. Therefore, a machine learning method will be developed for generating a computational model that could predict for a potential anti LprG activity of the novel antituberculosis compound. The present study will utilize dataset from PubChem database maintained by National Center for Biotechnology Information (NCBI). The dataset involves compounds screened against MTB were categorized as active and inactive based upon PubChem activity score. PowerMV, a molecular descriptor generator, and visualization tool will be used to generate the 2D molecular descriptors for the actives and inactive compounds present in the dataset. The 2D molecular descriptors generated from PowerMV will be used as features. We feed these features into three different classifiers, namely, random forest, a deep neural network, and a recurring neural network, to build separate predictive models and choosing the best performing model based on the accuracy of predicting novel antituberculosis compound with an anti LprG activity. Additionally, the efficacy of predicted active compounds will be screened using SMARTS filter to choose molecule with drug-like features.

Keywords: antituberculosis drug, classifier, machine learning, molecular descriptors, prediction

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Authors: Ladan Maijama’a, Jibril D. Jiya, Ejike C. Anene

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This paper presents Differential Evolution Algorithm (DEA) based Variable Structure Position Control (VSPC) of Laboratory DC servomotor (LDCSM). DEA is employed for the optimal tuning of Variable Structure Control (VSC) parameters for position control of a DC servomotor. The VSC combines the techniques of Sliding Mode Control (SMC) that gives the advantages of small overshoot, improved step response characteristics, faster dynamic response and adaptability to plant parameter variations, suppressed influences of disturbances and uncertainties in system behavior. The results of the simulation responses of the VSC parameters adjustment by DEA were performed in Matlab Version 2010a platform and yield better dynamic performance compared with the untuned VSC designed.

Keywords: differential evolution algorithm, laboratory DC servomotor, sliding mode control, variable structure control

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Surrogate model has received increasing attention for use in detecting damage of structures based on vibration modal parameters. However, uncertainties existing in the measured vibration data may lead to false or unreliable output result from such model. In this study, an efficient approach based on Monte Carlo simulation is proposed to take into account the effect of uncertainties in developing a surrogate model. The probability of damage existence (PDE) is calculated based on the probability density function of the existence of undamaged and damaged states. The kriging technique allows one to genuinely quantify the surrogate error, therefore it is chosen as metamodeling technique. Enhanced version of ideal gas molecular movement (EIGMM) algorithm is used as main algorithm for model updating. The developed approach is applied to detect simulated damage in numerical models of 72-bar space truss and 120-bar dome truss. The simulation results show the proposed method can perform well in probability-based damage detection of structures with less computational effort compared to direct finite element model.

Keywords: probability-based damage detection (PBDD), Kriging, surrogate modeling, uncertainty quantification, artificial intelligence, enhanced ideal gas molecular movement (EIGMM)

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Authors: Devi Eka Septiyani Arifin, Jrjeng Ruan

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As an approach to manipulate the performance of polymer thin film, epitaxy crystallization within polymer blends of poly(vinylidene fluoride) (PVDF) and its copolymer poly(vinylidene fluoride-trifluoroethylene) P(VDF-TrFE) was studied in this research, which involves the competition between phase separation and crystal growth of constitutive semicrystalline polymers. The unique piezoelectric feature of poly(vinylidene fluoride) crystalline phase is derived from the packing of molecular chains in all-trans conformation, which spatially arranges all the substituted fluorene atoms on one side of the molecular chain and hydrogen atoms on the other side. Therefore, the net dipole moment is induced across the lateral packing of molecular chains. Nevertheless, due to the mutual repulsion among fluorene atoms, this all-trans molecular conformation is not stable, and ready to change above curie temperature, where thermal energy is sufficient to cause segmental rotation. This research attempts to explore whether the epitaxial interactions between piezoelectric crystals and crystal lattice of hexamethylbenzene (HMB) crystalline platelet is able to stabilize this metastable all-trans molecular conformation or not. As an aromatic crystalline compound, the melt of HMB was surprisingly found able to dissolve the poly(vinylidene fluoride), resulting in homogeneous eutectic solution. Thus, after quenching this binary eutectic mixture to room temperature, subsequent heating or annealing processes were designed to explore the involve phase separation and crystallization behavior. The phase transition behaviors were observed in-situ by X-ray diffraction and differential scanning calorimetry (DSC). The molecular packing was observed via transmission electron microscope (TEM) and the principles of electron diffraction were brought to study the internal crystal structure epitaxially developed within thin films. Obtained results clearly indicated the occurrence of heteroepitaxy of PVDF/PVDF-TrFE on HMB crystalline platelet. Both the concentration of poly(vinylidene fluoride) and the mixing ratios of these two constitutive polymers have been adopted as the influential factors for studying the competition between the epitaxial crystallization of PVDF and P(VDF-TrFE) on HMB crystalline. Furthermore, the involved epitaxial relationship is to be deciphered and studied as a potential factor capable of guiding the wide spread of piezoelectric crystalline form.

Keywords: epitaxy, crystallization, crystalline platelet, thin film and mixing ratio

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Authors: Hamid Khachab, Yamani Abdelkafi, Mouna Barhmi

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The epitaxial growth has great important in the fabricate of the new semi-conductors devices and upgrading many factors, such as the quality of crystallization and efficiency with their deferent types and the most effective epitaxial technique is the molecular beam epitaxial. The MBE growth modeling allows to confirm the experiments results out by atomic beam and to analyze the microscopic phenomena. In of our work, we determined the growth processes specially the ZnSe epitaxial technique by Kinetic Monte Carlo method and we also give observations that are made in real time at the growth temperature using reflection high energy electron diffraction (RHEED) and photoemission current.

Keywords: molecular beam epitaxy, II-VI, morpholy, photoemission, RHEED, simulation, kinetic Monte Carlo, ZnSe

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Authors: Lethukuthula Ngobese, Abin Gupthar, Patrick Govender

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The ability of yeast cell wall-derived mannoproteins (glycoproteins) to positively contribute to oenological properties has been a key factor that stimulates research initiatives into these industrially important glycoproteins. In addition, and from a fundamental research perspective, yeast cell wall glycoproteins are involved in a wide range of biological interactions. To date, and to the best of our knowledge, our understanding of the fine molecular structure of these mannoproteins is fairly limited. Generally, the amino acid sequences of their protein moieties have been established from structural and functional analysis of the genomic sequence of these yeasts whilst far less information is available on the glycosyl moieties of these mannoproteins. A novel strategy was devised in this study that entails the genetic engineering of yeast strains that over-express and release cell wall-associated glycoproteins into the liquid growth medium. To this end, the Flo1p mannoprotein was overexpressed in Saccharomyces cerevisiae laboratory strains bearing a specific deletion in KNR4 and GPI7 genes involved in cell wall biosynthesis that have been previously shown to extracellularly hyper-secrete cell wall-associated glycoproteins. A polymerase chain reaction (PCR) -based cloning strategy was employed to generate transgenic yeast strains in which the native cell wall FLO1 glycoprotein-encoding gene is brought under transcriptional control of the constitutive PGK1 promoter. The modified Helm’s flocculation assay was employed to assess flocculation intensities of a Flo1p over-expressing wild type and deletion mutant as an indirect measure of their abilities to release the desired mannoprotein. The flocculation intensities of the transformed strains were assessed and all the strains showed similar intensities (>98% flocculation). To assess if mannoproteins were released into the growth medium, the supernatant of each strain was subjected to the BCA protein assay and the transformed Δknr4 strain showed a considerable increase in protein levels. This study has the potential to produce mannoproteins in sufficient quantities that may be employed in future investigations to understand their molecular structures and mechanisms of interaction to the benefit of both fundamental and industrial applications.

Keywords: glycoproteins, genetic engineering, flocculation, over-expression

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Authors: Meryem Imane Babaghayou, Abdelhafidi Asma

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This study deals with the ageing of Blown extruded films of low-density polyethylene (LDPE), used for greenhouse covering. The LDPE have been subjected to climatic ageing in a sub-Saharan facility at Laghouat (Algeria) with direct exposure to sun. The microstructural changes in the films were analyzed by IRFT for different states of ageing. The mechanical characterization was performed on a uniaxial tensile apparatus. The mechanical properties such as Young's modulus, strain at break, and stress at break have been followed for different states of exposure time (0 to 6 months). The Climatic ageing of LDPE films shows the effect of ageing on the microstructural Plan which leads to: i) To an oxidation of the molecular chains. ii) To the formation of cross-linkings and breaking chains, which both of them are responsible for the mechanical behavior’s modifications of the material. Cross-links are in favor of strengthening of the mechanical properties at break (the increase of σr and εr). In other side, the chains breaking leads to a decrease of these properties. The increase in the Young's modulus also seems to be related to those structural changes since the cross-links increase the average molecular weight. Branchings and tangles are favorable pairs for the ductile nature of the material. And in other side, the chains breaking reduces the average molecular weight and therefore promotes the stiffening (following to morphological changes) so the material becomes fragile. The post-mortem analysis of the samples shows that the mechanical stress has an effect on the molecular structure of the material. Although if quantitatively the concentrations of different chemical species exchanges, from a quantitative point of view only the unsaturations raises the polemics of a possible microstructural modification induced by mechanical stress applied during the tensile test. Also, we recommend a more rigorous analysis with other means of investigation.

Keywords: low-density polyethylene, ageing, mechanical properties, IRTF

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Authors: Fakhrosadat Sajjadian

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The majority of deaths in cancer patients are caused by distant metastasis. Breast cancer shows a unique spread pattern, often affecting bone, liver, lung, and brain. Breast cancer can be categorized into various subtypes according to gene expression patterns, and these subtypes exhibit specific preferences for organs where metastasis occurs. Breast tumors with luminal characteristics have a preference for spreading to the bone, whereas basal-like breast cancer (BLBC) shows a tendency to metastasize to the lungs. Still, the mechanisms behind this particular pattern of metastasis in organs have yet to be fully understood. In this evaluation, we will outline the latest progress in molecular signaling pathways and treatment methods for breast cancer lung metastasis.

Keywords: lung cancer, liver cancer, diagnosis, BLBC, metastasis

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Authors: Yuanhao Chang, Senbo Xiao, Zhiliang Zhang, Jianying He

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The role of nanoparticles (NPs) in enhanced oil recovery (EOR) is being increasingly emphasized. In this study, the motion of NPs and local stress distribution of tapped oil droplet/nanofluid in nanochannels are studied with coarse-grained modeling and molecular dynamic simulations. The results illustrate three motion patterns for NPs: hydrophilic NPs are more likely to adsorb on the channel and stay near the three-phase contact areas, hydrophobic NPs move inside the oil droplet as clusters and more mixed NPs are trapped at the oil-water interface. NPs in each pattern affect the flow of fluid and the interfacial thickness to various degrees. Based on the calculation of atomistic stress, the characteristic that the higher value of stress occurs at the place where NPs aggregate can be obtained. Different occurrence patterns correspond to specific local stress distribution. Significantly, in the three-phase contact area for hydrophilic NPs, the local stress distribution close to the pattern of structural disjoining pressure is observed, which proves the existence of structural disjoining pressure in molecular dynamics simulation for the first time. Our results guide the design and screen of NPs for EOR and provide a basic understanding of nanofluid applications.

Keywords: local stress distribution, nanoparticles, enhanced oil recovery, molecular dynamics simulation, trapped oil droplet, structural disjoining pressure

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Authors: Misbah Khan, Jian Wen, Muhammad Asif Shakoori

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The Organic Rankine Cycle (ORC) plays an important role in converting low-temperature heat sources into electrical power by using refrigerants as working fluids. The thermophysical properties of working fluids are essential for designing ORC. HFO-1336mzz(Z) (cis-1,1,1,4,4,4-hexafluoro-2-butene) considered as working fluid and have almost 99% low GWP and relatively same thermophysical properties used as a replacement of HFC-245fa (1,1,1,3,3-pentafluoro-propane). The environmental, safety, healthy and thermophysical properties of HFO-1336mzz(Z) are needed to use it in a practical system. In this paper, Molecular dynamics simulations were used to investigate the Homogeneous condensation, thermophysical and structural properties of HFO-1336mzz(Z) and HFC-245fa. The effect of various temperatures and pressures on thermophysical properties and condensation was extensively investigated. The liquid densities and isobaric heat capacities of this refrigerant was simulated at 273.15K to 353.15K temperatures and pressure0.5-4.0MPa. The simulation outcomes were compared with experimental data to validate our simulation method. The mean square displacement for different temperatures was investigated for dynamical analysis. The variations in potential energies and condensation rate were simulated to get insight into the condensation process. The radial distribution function was simulated at the micro level for structural analysis and revealed that the phase transition of HFO-1336mzz(Z) did not affect the intramolecular structure.

Keywords: homogenous condensation, refrigerants, molecular dynamics simulations, organic rankine cycle

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Authors: Yushinta Fujaya, Andi Ivo Asphama, Andi Parenrengi, Andi Tenriulo

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Blue Swimming crab (Portunus pelagicus) is an important commercial species throughout the subtropical waters and as such constitutes part of the fisheries resources. Data are lacking on the morphological variations of selected fast-growing crabs reared in a pond. This study aimed to analyze the morphological and molecular character of a selected fast-growing crab reared in ponds in South of Sulawesi. The crab seeds were obtained from local fish-trap and hatchery. A study on the growth was carried out in the population of crabs. The dimensions analyzed were carapace width (CW) measured after 3 months of grow out. Morphological character states were examined based on the pattern of spots on the carapace. Molecular analysis was performed using RAPD (Random Amplified Polymorphic DNA). Genetic distance was analysed using TFPGA (Tools for Population Genetic Analyses) version 1.3. The results showed that there were variations in the growth of crabs. These crabs clustered morphologically into three quite distinct groups. The crab with white spots irregularly spread over its carapace was the largest size while the crab with large white spots scattered over the carapace was the smaller size (3%). The crab with small white spots scattered over the carapace was the smallest size found in this study. Molecular analysis showed that there are morphologically and genetically different between groups of crabs. Genetic distances among crabs ranged from 0.1527 to 0.5856. Thus, this study provides information the use of white spots pattern over carapace as indicators to identify the type of blue swimming crabs.

Keywords: crab, portunus pelagicus, morphology, RAPD, Carapace

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Authors: Nermin Isik, Ozlem Derinbay Ekici

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Bovine coccidiosis is a protozoan disease caused by various species of Eimeria and most signs of disease are chronic or subclinical. The aim of this study was to determine the prevalence of Eimeria spp. in calves in Konya, in Turkey. The study, conducted from January- February 2015, involved 240 faecal samples of calves in the age groups of <1 month, 1-3 months and >3 months in Konya city centre, in Turkey. In a retrospective study from these faecal samples of calves submitted to the University of Selcuk, Faculty of Veterinary Medicine, Laboratory of Parasitology were evaluated regarding the prevalence of Eimeria spp. Faecal samples were examined by Fulleborn saturated salt floatation technique. Eimeria oocysts were found in 8.33% of all samples. The positivity rates in each of the age groups were different. According to the age groups (<1 month, 1-3 months and >3 months), the Eimeria spp. were determined as 0.83, 22.73 and 7.41%, respectively. After examination of stool, detected oocysts were sporulated in 2.5% potassium dichromate at 22º C and species were identified as E. cylindrica, E. zuernii, E. ellipsoidalis, E. subspherica, E. bovis, E. auburnensis, E. canadensis, E. illinoisensis and E. brasiliensis in infected calves. In conclusion, the highest prevalence was observed in the age group of 1-3 months. The presence of Eimeria species in calves demonstrated for the first time in the Konya region in Turkey. Other etiologic agents should also be investigated in calves more seriously. Further molecular epidemiological studies should be performed in this community.

Keywords: Eimeria spp., calves, diarrhea, bovine coccidiosis

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Authors: Irmak Karaduman, Tugba Corlu, Sezin Galioglu, Burcu Akata, M. Ali Yildirim, Aytunç Ateş, Selim Acar

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Breath analysis represents a promising non-invasive, fast and cost-effective alternative to well-established diagnostic and monitoring techniques such as blood analysis, endoscopy, ultrasonic and tomographic monitoring. Portable, non-invasive, and low-cost breath analysis devices are becoming increasingly desirable for monitoring different diseases, especially asthma. Beacuse of this, NO gas sensing at low concentrations has attracted progressive attention for clinical analysis in asthma. Recently, nanomaterials based sensors are considered to be a promising clinical and laboratory diagnostic tool, because its large surface–to–volume ratio, controllable structure, easily tailored chemical and physical properties, which bring high sensitivity, fast dynamic processand even the increasing specificity. Among various nanomaterials, semiconducting metal oxides are extensively studied gas-sensing materials and are potential sensing elements for breathanalyzer due to their high sensitivity, simple design, low cost and good stability.The sensitivities of metal oxide semiconductor gas sensors can be enhanced by adding noble metals. Doping contents, distribution, and size of metallic or metal oxide catalysts are key parameters for enhancing gas selectivity as well as sensitivity. By manufacturing doping MOS structures, it is possible to develop more efficient sensor sensing layers. Zeolites are perhaps the most widely employed group of silicon-based nanoporous solids. Their well-defined pores of sub nanometric size have earned them the name of molecular sieves, meaning that operation in the size exclusion regime is possible by selecting, among over 170 structures available, the zeolite whose pores allow the pass of the desired molecule, while keeping larger molecules outside.In fact it is selective adsorption, rather than molecular sieving, the mechanism that explains most of the successful gas separations achieved with zeolite membranes. In view of their molecular sieving and selective adsorption properties, it is not surprising that zeolites have found use in a number of works dealing with gas sensing devices. In this study, the Cu doped ZnO nanostructure film was produced by SILAR method and investigated the NO gas sensing properties. To obtain the selectivity of the sample, the gases including CO,NH3,H2 and CH4 were detected to compare with NO. The maximum response is obtained at 85 C for 20 ppb NO gas. The sensor shows high response to NO gas. However, acceptable responses are calculated for CO and NH3 gases. Therefore, there are no responses obtain for H2 and CH4 gases. Enhanced to selectivity, Cu doped ZnO nanostructure film was coated with zeolite A thin film. It is found that the sample possess an acceptable response towards NO hardly respond to CO, NH3, H2 and CH4 at room temperature. This difference in the response can be expressed in terms of differences in the molecular structure, the dipole moment, strength of the electrostatic interaction and the dielectric constant. The as-synthesized thin film is considered to be one of the extremely promising candidate materials in electronic nose applications. This work is supported by The Scientific and Technological Research Council of Turkey (TUBİTAK) under Project No, 115M658 and Gazi University Scientific Research Fund under project no 05/2016-21.

Keywords: Cu doped ZnO, electrical characterization, gas sensing, zeolite

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Authors: Man-Yun Liu, Emily Chia-Yu Su

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Alzheimer's disease (AD) is the public health crisis of the 21st century. AD is a degenerative brain disease and the most common cause of dementia, a costly disease on the healthcare system. Unfortunately, the cause of AD is poorly understood, furthermore; the treatments of AD so far can only alleviate symptoms rather cure or stop the progress of the disease. Currently, there are several ways to diagnose AD; medical imaging can be used to distinguish between AD, other dementias, and early onset AD, and cerebrospinal fluid (CSF). Compared with other diagnostic tools, blood (plasma) test has advantages as an approach to population-based disease screening because it is simpler, less invasive also cost effective. In our study, we used blood biomarkers dataset of The Alzheimer’s disease Neuroimaging Initiative (ADNI) which was funded by National Institutes of Health (NIH) to do data analysis and develop a prediction model. We used independent analysis of datasets to identify plasma protein biomarkers predicting early onset AD. Firstly, to compare the basic demographic statistics between the cohorts, we used SAS Enterprise Guide to do data preprocessing and statistical analysis. Secondly, we used logistic regression, neural network, decision tree to validate biomarkers by SAS Enterprise Miner. This study generated data from ADNI, contained 146 blood biomarkers from 566 participants. Participants include cognitive normal (healthy), mild cognitive impairment (MCI), and patient suffered Alzheimer’s disease (AD). Participants’ samples were separated into two groups, healthy and MCI, healthy and AD, respectively. We used the two groups to compare important biomarkers of AD and MCI. In preprocessing, we used a t-test to filter 41/47 features between the two groups (healthy and AD, healthy and MCI) before using machine learning algorithms. Then we have built model with 4 machine learning methods, the best AUC of two groups separately are 0.991/0.709. We want to stress the importance that the simple, less invasive, common blood (plasma) test may also early diagnose AD. As our opinion, the result will provide evidence that blood-based biomarkers might be an alternative diagnostics tool before further examination with CSF and medical imaging. A comprehensive study on the differences in blood-based biomarkers between AD patients and healthy subjects is warranted. Early detection of AD progression will allow physicians the opportunity for early intervention and treatment.

Keywords: Alzheimer's disease, blood-based biomarkers, diagnostics, early detection, machine learning

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Authors: R. Pérez Castells, J. M. Carbajo

Abstract:

Sepiolite is used as a processing aid in the manufacture of fibre cement from the start of the replacement of asbestos in the 80s. Sepiolite increases the inter-laminar bond between cement layers and improves homogeneity of the slurries. A new type of sepiolite processed product, Wollatrop TF/C, has been checked as a retention agent for fine particles in the production of fibre cement in a Hatschek machine. The effect of Wollatrop T/FC on filtering and fine particle losses was studied as well as the interaction with anionic polyacrylamide and microsilica. The design of the experiments were factorial and the VDT equipment used for measuring retention and drainage was modified Rapid Köethen laboratory sheet former. Wollatrop TF/C increased the fine particle retention improving the economy of the process and reducing the accumulation of solids in recycled process water. At the same time, drainage time increased sharply at high concentration, however drainage time can be improved by adjusting APAM concentration. Wollatrop TF/C and microsilica are having very small interactions among them. Microsilica does not control fine particle losses while Wollatrop TF/C does efficiently. Further research on APAM type (molecular weight and anionic character) is advisable to improve drainage.

Keywords: drainage, fibre-reinforced cement, fine particle losses, flocculation, microsilica, sepiolite

Procedia PDF Downloads 326

Authors: Elmira Ghanbari, Jan Van Esch, Stephen J. Picken, Sahil Aggarwal

Abstract:

Low-molecular-weight organogelators form gels by self-assembly into the crystalline network which immobilizes the organic solvent. For single bisamide organogelator systems, the effect of the molecular structure on the molecular interaction and their self-assembly behavior has been explored. The spatial arrangement of bisamide molecules in the gel-state is driven by a combination of hydrogen bonding and Van der Waals interactions. The hydrogen-bonding pattern between the amide groups of bisamide molecules is regulated by the number of methylene spacers; the even number of methylene spacers between two amide groups, in even-spaced bisamides, leads to the antiparallel position of amide groups within a molecule. An even-spaced bisamide molecule with antiparallel amide groups can make two pairs of hydrogen bonding with the molecules on the same plane. The odd-spaced bisamide with a parallel directionality of amide groups can form four independent hydrogen bonds with four other bisamide molecules on different planes. The arrangement of bisamide molecules in the crystalline state and the interaction of these molecules depends on the molecular structure, particularly the parity of the spacer length between the amide groups in the bisamide molecule. In this study, the directionality of amide groups has been exploited as a structural characteristic to affect the arrangement of molecules in the crystalline state and produce different binary bisamide gelators with different degrees of crystallinities. Single odd- and even-spaced single bisamides were synthesized and blended to produce binary bisamide organogelators to be characterized in order to understand the effect of the different directionality of amide groups on the molecular interaction in the crystalline state. The pattern of molecular interactions between these blended molecules, mixing or phase separation, has been monitored via differential scanning calorimetry (DSC) and crystallography techniques; X-ray powder diffraction (XRD) and Small-angle X-ray scattering (SAXS). The formation of lamellar structures for odd- and even-spaced bisamide gelators was confirmed by using SAXS and XRD techniques. DSC results have shown that binary bisamide organogelators with different parity of methylene spacers (odd-even binary blends) have a higher tendency for phase separation compared to the binary bisamides with the same parity (odd-odd or even-even binary blends). Phase separation in binary odd-even bisamides was confirmed by the presence of individual (100) reflections of odd and even lamellar structures. The structural characteristic of bisamide organogelators, the parity of spacer length in binary systems, is a promising tool to control the arrangement of molecules and their crystalline structure.

Keywords: binary bisamide organogelators, crystalline structure, phase separation, self-assembly behavior

Procedia PDF Downloads 185

Authors: Rauan Sakenov, Peter Bukovics, Peter Gaszler, Veronika Tokacs-Kollar, Beata Bugyi

Abstract:

FH2 (formin homology-2) domains of several proteins, collectively known as formins, including DAAM, DAAM1 and mDia1, promote G-actin nucleation and elongation. FH2 domains of these formins exist as oligomers. Chain dimerization by ring structure formation serves as a structural basis for actin polymerization function of FH2 domain. Proper single chain configuration and specific interactions between its various regions are necessary for individual chains to form a dimer functional in G-actin nucleation and elongation. FH1 and WH2 domain-containing formins were shown to behave as intrinsically disordered proteins. Thus, the aim of this research was to study structural dynamics of FH2 domain of DAAM. To investigate structural features of FH2 domain of DAAM, molecular dynamics simulation of chain A of FH2 domain of DAAM solvated in water box in 50 mM NaCl was conducted at temperatures from 293.15 to 353.15K, with VMD 1.9.2, NAMD 2.14 and Amber Tools 21 using 2z6e and 1v9d PDB structures of DAAM was obtained on I-TASSER webserver. Calcium and ATP bound G-actin 3hbt PDB structure was used as a reference protein with well-described structural dynamics of denaturation. Topology and parameter information of CHARMM 2012 additive all-atom force fields for proteins, carbohydrate derivatives, water and ions were used in NAMD 2.14 and ff19SB force field for proteins in Amber Tools 21. The systems were energy minimized for the first 1000 steps, equilibrated and produced in NPT ensemble for 1ns using stochastic Langevin dynamics and the particle mesh Ewald method. Our root-mean square deviation (RMSD) analysis of molecular dynamics of chain A of FH2 domains of DAAM revealed similar insignificant changes of total molecular average RMSD values of FH2 domain of these formins at temperatures from 293.15 to 353.15K. In contrast, total molecular average RMSD values of G-actin showed considerable increase at 328K, which corresponds to the denaturation of G-actin molecule at this temperature and its transition from native, ordered, to denatured, disordered, state which is well-described in the literature. RMSD values of lasso and tail regions of chain A of FH2 domain of DAAM exhibited higher than total molecular average RMSD at temperatures from 293.15 to 353.15K. These regions are functional in intra- and interchain interactions and contain highly conserved tryptophan residues of lasso region, highly conserved GNYMN sequence of post region and amino acids of the shell of hydrophobic pocket of the salt bridge between Arg171 and Asp321, which are important for structural stability and ordered state of FH2 domain of DAAM and its functions in FH2 domain dimerization. In conclusion, higher than total molecular average RMSD values of lasso and post regions of chain A of FH2 domain of DAAM may explain disordered state of FH2 domain of DAAM at temperatures from 293.15 to 353.15K. Finally, absence of marked transition, in terms of significant changes in average molecular RMSD values between native and denatured states of FH2 domain of DAAM at temperatures from 293.15 to 353.15K, can make it possible to attribute these formins to the group of intrinsically disordered proteins rather than to the group of intrinsically ordered proteins such as G-actin.

Keywords: FH2 domain, DAAM, formins, molecular modelling, computational biophysics

Procedia PDF Downloads 136

Authors: Richa Dhingra, Monika, Manav Malhotra, Tilak Raj Bhardwaj, Neelima Dhingra

Abstract:

5-Alpha-reductases (5AR), a membrane bound, NADPH dependent enzyme and convert male hormone testosterone (T) into more potent androgen dihydrotestosterone (DHT). DHT is the required for the development and function of male sex organs, but its overproduction has been found to be associated with physiological conditions like Benign Prostatic Hyperplasia (BPH). Thus the inhibition of 5ARs could be a key target for the treatment of BPH. In present study, 2D and 3D Quantitative Structure Activity Relationship (QSAR) pharmacophore models have been generated for 5AR based on known inhibitory concentration (IC₅₀) values with extensive validations. The four featured 2D pharmacophore based PLS model correlated the topological interactions (–OH group connected with one single bond) (SsOHE-index); semi-empirical (Quadrupole2) and physicochemical descriptors (Mol. wt, Bromines Count, Chlorines Count) with 5AR inhibitory activity, and has the highest correlation coefficient (r² = 0.98, q² =0.84; F = 57.87, pred r² = 0.88). Internal and external validation was carried out using test and proposed set of compounds. The contribution plot of electrostatic field effects and steric interactions generated by 3D-QSAR showed interesting results in terms of internal and external predictability. The well validated 2D Partial Least Squares (PLS) and 3D k-nearest neighbour (kNN) models were used to search novel 5AR inhibitors with different chemical scaffold. To gain more insights into the molecular mechanism of action of these steroidal derivatives, molecular docking and in silico absorption, distribution, metabolism, and excretion (ADME) studies were also performed. Studies have revealed the hydrophobic and hydrogen bonding of the ligand with residues Alanine (ALA) 63A, Threonine (THR) 60A, and Arginine (ARG) 456A of 4AT0 protein at the hinge region. The results of QSAR, molecular docking, in silico ADME studies provide guideline and mechanistic scope for the identification of more potent 5-Alpha-reductase inhibitors (5ARI).

Keywords: 5α-reductase inhibitor, benign prostatic hyperplasia, ligands, molecular docking, QSAR

Procedia PDF Downloads 163

Authors: Y. Z. Gad

Abstract:

Disorders of Sex Development (DSD) are defined as congenital conditions in which development of chromosomal, gonadal or anatomical sex is atypical. The DSD are relatively prevalent in Egypt. In spite of that, the relative rarity of the individual disease types or their molecular pathologies frequently resulted in reporting on single or few cases. This augmented the challenging nature of phenotype-genotype correlation in this disease group and its utilization in the management of such medical emergency. Through critical assessment of the published DSD reports, the current review aims at analyzing the clinical characteristics of the various DSD forms in relation to the underlying molecular pathologies. A systematic literature search was done in Pubmed, using relevant keywords (Egypt versus DSD, genital ambiguity or ambiguous genitalia, the old terms of 'intersex, hermaphroditism and pseudohermaphroditism', and a list of the DSD entities and their related genes). The search yielded 24 reports of molecular data in Egyptian patients presenting with ambiguous genitalia. However, only 21 publications fulfilled the criteria of inclusion of detailed clinical descriptions and definitive molecular diagnoses of individual patients. Curation of the data yielded a total of 53 cases that were ascertained from 40 families. Fifty-one patients present with ambiguous genitalia only while 2 had multiple congenital anomalies. Parental consanguinity was noted in 60% of cases. Sex of rearing at initial presentation was female in 75% and 60% in 46,XY and 46,XX DSD cases, respectively. The external genital phenotype in 2/3 of the 46,XY DSD cases showed moderate undermasculinization [Quigley scores 3 & 4] and 1/3 had severe presentations [scores 5 & 6]. For 46,XX subjects, 1 had severe virilization of the external genitalia while 8 had moderate phenotype. Hormonal data were inconclusive or contradictory to final diagnosis in a forth of cases. Collectively, 31 families [31/40, 77.5%] with 46,XY DSD had molecular defects in the genes, 5 alpha reductase 2 (SRD5A2) [12/31], 17 beta-hydroxysteroid dehydrogenase 3 [8/31], androgen receptor [7/31], Steroidogenic factor 1 [2/31], luteinizing hormone receptor [1/31], and fibroblast growth factor receptor 1 [1/31]. In a multiethnic study, 9 families afflicted with 46,XX DSD due to 11 beta hydroxylase (CYP11B1) deficiency were documented. Two recurrent mutations, G34R and N160D, in SRD5A2 were present, respectively, in 42 and 17% of cases. Similarly, 4 recurrent mutations resulted in 89% of the CYP11B1 presentations. In conclusion, this analysis highlights the importance of autosomal recessive inheritance and inbreeding among DSD presentations, the importance of founder effect in at least 2 disorders, the difficulties in relating the genotype with the indeterminate genital phenotype, the under-reporting of some DSD subtypes, and the notion that the reported mutational profiles among Egyptian DSD cases are relatively different from those reported in other ethnic groups.

Keywords: disorders of sex development, genital ambiguity, mutation, molecular diagnosis, Egypt

Procedia PDF Downloads 137

Authors: Chunyang Miao, Bingxin Li, Shanglong Ning, Christopher J. B. Ford

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While it is challenging to fabricate electronic devices close to atomic dimensions in conventional top-down lithography, molecular electronics is promising to help maintain the exponential increase in component densities via using molecular building blocks to fabricate electronic components from the bottom up. It offers smaller, faster, and more energy-efficient electronic and photonic systems. A self-assembled monolayer (SAM) of molecules is a layer of molecules that self-assembles on a substrate. They are mechanically flexible, optically transparent, low-cost, and easy to fabricate. A large-area multi-layer structure has been designed and investigated by the team, where a SAM of designed molecules is sandwiched between graphene and gold electrodes. Each molecule can act as a quantum dot, with all molecules conducting in parallel. When a source-drain bias is applied, significant current flows only if a molecular orbital (HOMO or LUMO) lies within the source-drain energy window. If electrons tunnel sequentially on and off the molecule, the charge on the molecule is well-defined and the finite charging energy causes Coulomb blockade of transport until the molecular orbital comes within the energy window. This produces ‘Coulomb diamonds’ in the conductance vs source-drain and gate voltages. For different tunnel barriers at either end of the molecule, it is harder for electrons to tunnel out of the dot than in (or vice versa), resulting in the accumulation of two or more charges and a ‘Coulomb staircase’ in the current vs voltage. This nanostructure exhibits highly reproducible Coulomb-staircase patterns, together with additional oscillations, which are believed to be attributed to molecular vibrations. Molecules are more isolated than semiconductor dots, and so have a discrete phonon spectrum. When tunnelling into or out of a molecule, one or more vibronic states can be excited in the molecule, providing additional transport channels and resulting in additional peaks in the conductance. For useful molecular electronic devices, achieving the optimum orbital alignment of molecules to the Fermi energy in the leads is essential. To explore it, a drop of ionic liquid is employed on top of the graphene to establish an electric field at the graphene, which screens poorly, gating the molecules underneath. Results for various molecules with different alignments of Fermi energy to HOMO have shown highly reproducible Coulomb-diamond patterns, which agree reasonably with DFT calculations. In summary, this large-area SAM molecular junction is a promising candidate for future electronic circuits. (1) The small size (1-10nm) of the molecules and good flexibility of the SAM lead to the scalable assembly of ultra-high densities of functional molecules, with advantages in cost, efficiency, and power dissipation. (2) The contacting technique using graphene enables mass fabrication. (3) Its well-observed Coulomb blockade behaviour, narrow molecular resonances, and well-resolved vibronic states offer good tuneability for various functionalities, such as switches, thermoelectric generators, and memristors, etc.

Keywords: molecular electronics, Coulomb blokade, electron-phonon coupling, self-assembled monolayer

Procedia PDF Downloads 63

Authors: Elisa Y. M. Ang, Teng Yong Ng, Jingjie Yeo, Rongming Lin, Zishun Liu, K. R. Geethalakshmi

Abstract:

By stacking carbon nanotubes (CNT) one on top of another, single layer CNT arrays can perform water-salt separation with ultra-high permeability and selectivity. Such outer-wall CNT slit membrane is named as the transverse flow CNT membrane. By adjusting the slit size between neighboring CNTs, the membrane can be configured to sieve out different solutes, right down to the separation of monovalent salt ions from water. Molecular dynamics (MD) simulation results show that the permeability of transverse flow CNT membrane is more than two times that of conventional axial-flow CNT membranes, and orders of magnitude higher than current reverse osmosis membrane. In addition, by carrying out MD simulations with different CNT size, it was observed that the variance in desalination performance with CNT size is small. This insensitivity of the transverse flow CNT membrane’s performance to CNT size is a distinct advantage over axial flow CNT membrane designs. Not only does the membrane operate well under constant pressure desalination operation, but MD simulations further indicate that oscillatory operation can further enhance the membrane’s desalination performance, making it suitable for operation such as electrodialysis reversal. While there are still challenges that need to be overcome, particularly on the physical fabrication of such membrane, it is hope that this versatile membrane design can bring the idea of using low dimensional structures for desalination closer to reality.

Keywords: carbon nanotubes, membrane desalination, transverse flow carbon nanotube membrane, molecular dynamics

Procedia PDF Downloads 196

Authors: Huda Qari, I. A. Hassan

Abstract:

The brown alga Padina boryanawas was used for bioassay of polycyclic aromatic hydrocarbons (PAHs) accumulation at the seashore of Jeddah city. PAHs were determined in the coastal water and algal tissues by GC-MS. Acenaphthene (Ace) and dibenzo (a,h) anthracene (dB(a,h)An) were the main PAHs in seawater (50.02 and 46.18) and algal tissues (64.67 and 72.45), respectively. The ratios of low molecular weight/high molecular weight hydrocarbons (1.76 – 1.44), fluoranthene/pyrene (1.57 – 1.52) and phenanthrene/anthracene (0.86 – 0.67) in seawater and algal tissues, respectively, indicated the origin of the PAHs to be mainly petrogenic. This study has demonstrated the utility of using Padina boryanawas as a biomonitor of PAH contamination and bioavailability in the coastal waters.

Keywords: polycyclic aromatic hydrocarbons, Padina boryanawas, bioaccumulation, waste water

Procedia PDF Downloads 285