Search results for: molecular differentiation

Authors: Alexis John de Britto

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Studies were performed to select the superior genotypes based on intra-specific variations, caused by phytogeographical, climatic and edaphic parameters of three anti cancer drug yielding mangrove plants such as Acanthus ilicifolius L., Calophyllum inophyllum L. and Excoecaria agallocha L. using ISSR (Inter Simple Sequence Repeats) markers and phytochemical analysis such as preliminary phytochemical tests, TLC, HPTLC, HPLC and antioxidant tests. The plants were collected from five different geographical locations of the East Coast of south India. Genetic heterozygosity, Nei’s gene diversity, Shannon’s information index and Percentage of polymorphism between the populations were calculated using POPGENE software. Cluster analysis was performed using UPGMA algorithm. AMOVA and correlations between genetic diversity and soil factors were analyzed. Combining the molecular and phytochemical variations superior genotypes were selected. Conservation constraints and methods of efficient exploitation of the species are discussed.

Keywords: anti-cancer drug yielding plants, DNA fingerprinting, phytochemical analysis, selection of superior genotypes

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Authors: Dwi Yulian Fahruddin Shah, Salman Al Farizi, Elyada Ahastari Liunome

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Indonesia is a multicultural society. A wide variety of arts and culture spread throughout in all of part of Indonesia with natural appearance will cause the social behavior differentiation. Similarly, with Tengger people's lives also have different social behaviors that distinguish them from other ethnic groups spread across the Indonesian archipelago. Tengger tribe has an appropriate ethic to build nation character. If all the people of Indonesia who heterogeneous and multicultural can understand, and follow the example of ethical behavior of Tengger tribe, it will be a force in the development of the character of the nation in this modern and globalization era.

Keywords: Tengger tribe, national character, ethics society, Indonesia

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Authors: Said Ghalem

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Honey is primarily composed of sugars: glucose and fructose. Depending honey, it's either fructose or glucose predominates. More the fructose concentration and the less the glycemic index (GI) is high. Thus, changes in the insulin response shows a decrease of the amount of insulin secreted at an increased fructose honey. Honey is also a compound that can reduce the lipid in the blood. Several studies on animals, but which remain to be checked in humans, have shown that the honey can have interesting effects when combined with other molecules: associated with Metformin (a medicine taken by diabetics), it shows the benefits and effects of diabetes preserves the tissue; associated ginger, it increases the antioxidant activity and thus avoids neurologic complications, neuropathic. Molecular modeling techniques are widely used in chemistry, biology, and the pharmaceutical industry. Most of the currently existing drugs target enzymes. Inhibition of DPP-4 is an important approach in the treatment of type 2 diabetes. We have chosen for the inhibition of DPP-4 the following molecules: Linagliptin (BI1356), Sitagliptin (Januvia), Vildagliptin, Saxagliptin, Alogliptin, and Metformin (Glucophage), that are involved in the disease management of type 2 diabetes and added to honey. For this, we used software Molecular Operating Environment. A Wistar rat study was initiated in our laboratory with a well-studied protocol; after sacrifice, according to international standards and respect for the animal This theoretical approach predicts the mode of interaction of a ligand with its target. The honey can have interesting effects when combined with other molecules, it shows the benefits and effects of honey preserves the tissue, it increases the antioxidant activity, and thus avoids neurologic complications, neuropathic or macrovascular. The organs, especially the kidneys of Wistar, shows that the parameters to renal function let us conclude that damages caused by diabetes are slightly perceptible than those observed without the addition of a high concentration of fructose honey.

Keywords: honey, molecular modeling, DPP4 enzyme, metformin

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Authors: Manal Alhazmi, Artem Mishchenko

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A molecular fluids' behavior and interaction with other materials at the nanoscale is a complex process. Nanoscale fluids behave so differently than macroscale fluids and interact with other materials in unique ways. It is, therefore, feasible to understand the molecular behavior of H₂O in such two-dimensional nanoscale systems by studying (CaSO4-2H2O), commonly known as gypsum. In the present study, spectroscopic measurements on a 2D structure of exfoliated gypsum crystals are carried out by Raman and IR spectroscopy. An array of gypsum flakes with thicknesses ranging from 8nm to 100nm were observed and analyzed for their Raman and IR spectrum. Water molecules stretching modes spectra lines were also measured and observed in nanoscale gypsum flakes and compared with those of bulk crystals. CaSO4-2H2O crystals have Raman and infrared bands at 3341 cm-1 resulting from the weak hydrogen bonds between the water molecules. This internal vibration of water molecules, together with external vibrations with other atoms, are responsible for these bands. There is a shift of about 70 cm-1 In the peak position of thin flakes with respect to the bulk crystal, which is a result of the different atomic arrangement from bulk to thin flake on the nano scale. An additional peak was observed in Raman spectra around 2910-3137 cm⁻¹ in thin flakes but is missing in bulk crystal. This additional peak is attributed to a combined mode of water internal (stretching mode at 3394cm⁻¹) and external vibrations. In addition to Raman and infra- red analysis of gypsum 2D structure, electrical measurements were conducted to reveal the water molecules transport behavior in such systems. Electrical capacitance of the fabricated device is measured and found to be (0.0686 *10-12) F, and the calculated dielectric constant (ε) is (12.26).

Keywords: gypsum, infra-red spectroscopy, raman spectroscopy, H₂O behavior

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Authors: Hong Su, Qiuju Yan, Wei Du, En Hu, Zhaoyu Yang, Wei Zhang, Yusheng Li, Tao Tang, Wang yang, Shushan Zhao

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Osteoarthritis (OA) is a severe chronic inflammatory disease. As the main active component of Astragalus mongholicus Bunge, a classic traditional ethnic herb, calycosin exhibits anti-inflammatory action and its mechanism of exact targets for OA have yet to be determined. In this study, we established an anterior cruciate ligament transection (ACLT) mouse model. Mice were randomized to sham, OA, and calycosin groups. Cartilage synthesis markers type II collagen (Col-2) and SRY-Box Transcription Factor 9 (Sox-9) increased significantly after calycosin gavage. While cartilage matrix degradation index cyclooxygenase-2 (COX-2), phosphor-epidermal growth factor receptor (p-EGFR), and matrix metalloproteinase-9 (MMP9) expression were decreased. With the help of network pharmacology and molecular docking, these results were confirmed in chondrocyte ATDC5 cells. Our results indicated that the calycosin treatment significantly improved cartilage damage, this was probably attributed to reversing the imbalance between chondrocyte synthesis and catabolism.

Keywords: calycosin, osteoarthritis, network pharmacology, molecular docking, inflammatory, cyclooxygenase 2

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Authors: T. Abohalkuma, J. Telegdi

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Preparation, characterization, and application of self-assembled monolayers (SAM) formed by fluorophosphonic and undecenyl phosphonic acids on carbon steel surfaces as anticorrosive nanocoatings were demonstrated. The anticorrosive efficacy of these SAM layers was followed by atomic force microscopy, as the change in the surface morphology caused by layer deposition and corrosion processes was monitored. The corrosion process was determined by electrochemical potentiodynamic polarization, whereas the surface wettability of the carbon steel samples was tested with the use of static and dynamic contact angle measurements. Results showed that both chemicals produced good protection against corrosion as they performed as anodic inhibitors, especially with increasing the time of layer formation, which results in a more compact molecular film. According to the atomic force microscope (AFM) images, the fluoro-phosphonic acid self-assembled molecular layer can control the general as well as the pitting corrosion, but the SAM layers of the undecenyl-phosphonic acid cannot inhibit the pitting corrosion. The AFM and the contact angle measurements confirmed the results achieved by electrochemical measurements.

Keywords: nanolayers, corrosion, phosphonic acids, coatings

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Authors: Suliman A. I. Ali, Mory Mandiana Diakite, Saqib Ali, Man-Qun Wang

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Lesser grain borer, Rhyzopertha dominica, is a causing damages of stored grains all tropical and subtropical area in the global, according to the information of antenna cDNA library of R. dominica, three olfactory protein genes, including R.domica CSPs2, R.domica PBPs1, R.domica PBPs2 genes (GenBank accessions are KJ186798.1, KJ186830.1, KJ186831.1 separately.), were successfully cloned. For sequencing and phylogenetic analysis, R.domica CSPs1 and R.domica CSPs2 belonged to Minus-C CSPs showed that have 4 conserved cysteine residues, while R.domica PBPs1 and R.domica PBPs2 showed conserved amino acids in all PBPs six conserved cysteine residues. The results of transcription expression level of PBPs1 and PBPs2 of R. dominica showed that the expression level of R.domnica PBP2 is much higher than that of R.domnica PBP1. The variation transcription level at the different developmental time suggested the PBP1, and PBP2 had their particular job in searching food sources, mates and oviposition sites.

Keywords: Rhyzopertha dominica, CSPs, PBPs, molecular cloning

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Authors: Mariam Shah

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Strict liability is frequently used in magistrate’s courts for TV license and driving offences.There is existing research suggesting that the strict liability approach to criminal offences can result in ‘absurd’ judicial outcomes, or potentially ‘injustice’.This paper will discuss the potential merits of strict liability as a method for dealing with shoplifting offences.Currently, there is disparity in sentencing outcomes in the UK, particularly in relation to shoplifting offences.This paper will question whether ‘injustice’ is actually in the differentiation of defendants based upon their ‘perceived’ circumstances, which could be resulting in arbitrary judicial decision making.

Keywords: arbitrary, decision making, judicial decision making, shoplifting, stereotypes, strict liability

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Authors: Iyad Jadalhaq, Mohammed El Hadi El Maknouzi

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The place of Islamic law in the legal system of the UAE is best understood by introducing a differentiation between its role as a formal source of law and its influence as a material source of law. What this differentiation helps clarify is that the corpus of Islamic law constitutes a much deeper influence on adjudication, law-making and the legal profession in the UAE, than it might appear at first sight, by considering its formal position in the division of labor between courts, or legislative lists of sources of law. This paper aims to examine the role of Shariah in the UAE private law system by determining the comprehensiveness of Sharia in the legal system as a whole, and not in a limited way related to it as a source of law according to Article 1 of the Civil Transactions Law. Turning to the role of the Shariah as a formal source of law, it is useful to start from Article 1 of the UAE Civil Code. This provision lays out the formal hierarchy of sources of UAE private law, these being legislation, Islamic law, and custom. Hence, when deciding a civil dispute, a judge should first refer to positive legislation in force in the UAE. Lacking the rule to cover the case before him/her, the judge ought then to refer directly to Islamic law. If the matter lacks regulation in Islamic law, only then may the judge appeal to custom. Accordingly, in connection to civil transactions, Shariah is presented here, formally, as the second source of law. Still, Shariah law addresses many other issues beyond civil transactions, including matters of morals, worship, and belief. However, in Article 1 of the UAE Civil Code, the reference to Islamic law ought to be understood as limited to the rules it lays out for civil transactions. There are four main sets of courts in the judicial systems of the UAE, whose competence is based on whether a dispute touches upon civil and commercial transactions, criminal offenses, personal statuses, or labor relations. This sectorial and multi-tiered organization of courts as a whole constitutes an institutional development compatible with the long-standing affirmation in the Shariah of the legitimacy of the judiciary. Indeed, Islamic law authorizes the governing authorities to organize the judiciary, including by allocating specific types of cases to particular kinds of judges depending on the value of the case, or by assigning judges to a specific place in which they are to exercise their jurisdictional function. In view of this, the contemporary organization of courts in the UAE can be regarded as an organic adaptation, aligned with Shariah rules on the assignment of jurisdictional authority, to the growing complexity of modern society. Therefore, we can conclude to the comprehensive role of Shariah in the entire legal system of the United Arab Emirates, including legislation, a judicial system, institutional, and administrative work.

Keywords: Islamic jurisprudence, Shariah, UAE civil code, UAE private law

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Authors: Nariman Shahhosseini, Sadegh Chinikar

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Introduction: Crimean-Congo hemorrhagic fever virus (CCHFV) causes severe disease with fatality rates of 30%. The virus is transmitted to humans through the bite of an infected tick, direct contact with the products of infected livestock and nosocomially. The disease occurs sporadically throughout many of African, Asian, and European countries. Different species of ticks serve either as vector or reservoir for CCHFV. Materials and Methods: A molecular survey was conducted on hard ticks (Ixodidae) in Golestan province, north of Iran during 2014-2015. Samples were sent to National Reference Laboratory of Arboviruses (Pasteur Institute of Iran) and viral RNA was detected by RT-PCR. Results: Result revealed the presence of CCHFV in 5.3% of the selected ticks. The infected ticks belonged to Hy. dromedarii, Hy. anatolicum, Hy. marginatum, and Rh. sanguineus. Conclusions: These data demonstrates that Hyalomma ticks are the main vectors of CCHFV in Golestan province. Thus, preventive strategies such as using acaricides and repellents in order to avoid contact with Hyalomma ticks are proposed. Also, personal protective equipment (PPE) must be utilized at abattoirs.

Keywords: tick, CCHFV, surveillance, vector diversity

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Authors: Merouane Salhi, Toufik Zebbiche

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When the stagnation pressure of perfect gas increases, the specific heat and their ratio do not remain constant anymore and start to vary with this pressure. The gas doesn’t remain perfect. Its state equation change and it becomes for a real gas. In this case, the effects of molecular size and intermolecular attraction forces intervene to correct the state equation. The aim of this work is to show and discuss the effect of stagnation pressure on supersonic thermodynamical, physical and geometrical flow parameters, to find a general case for real gas. With the assumptions that Berthelot’s state equation accounts for the molecular size and intermolecular force effects, expressions are developed for analyzing supersonic flow for thermally and calorically imperfect gas lower than the dissociation molecules threshold. The designs parameters for supersonic nozzle like thrust coefficient depend directly on stagnation parameters of the combustion chamber. The application is for air. A computation of error is made in this case to give a limit of perfect gas model compared to real gas model.

Keywords: supersonic flow, real gas model, Berthelot’s state equation, Simpson’s method, condensation function, stagnation pressure

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Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

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Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

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Authors: John Onolame Unuofin, Uchechukuw U. Nwodo, Anthony I. Okoh

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Laccase is constantly gaining status as important biocatalyst in biotechnology. The illimitable potential of its industrial applications and the corresponding aggressive need for phenomenal volumes of extracellularly secreted laccases have called for its interminable production from sources which are able to meet this demand within a relatively short period of time, preferably bacteria. In response to this call, this study was designed to source for laccase-producing bacteria from different environmental matrices. Three sampling environments were chosen such as wastewater treatment plants, University of Fort Hare vicinity and the Hogback woodland, all within the Eastern Cape, South Africa. Samples such as effluents, sediments, leaf litters, degrading wood and rock scrapings were selectively enriched with some model aromatic compounds and were further screened qualitatively and quantitatively on five phenolic substrates ABTS (2,2’-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid), Guaiacol, 1-Naphthol, Potassium Ferric Cyanide and Syringaldazine). Basis for selection was their ability to elicit a colour change on at least three of the above mentioned agar based assay substrates. The choice isolates were further identified based on 16S rRNA molecular identification techniques. 33 isolates were screened out of the 40 representative distinct colonies during the qualitative plate screens, while quantitative screens selected out 11 bacterial isolates. They were, based on molecular identification, desginated as members of the genera Pseudomonas, Stenotrophomonas and Citrobacter of the gammaproteobacteria and Bordetalla and Achromobacter of the betaproteobacteria respectively. We therefore conclude based on our outcomes that we may have isolated efficient laccase-producing bacteria, which might be of beneficial significance in catalysis and biotechnology.

Keywords: beta proteobacteria, catalysis, gammaproteobacteria, laccase

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Authors: Dalal Alghawas, Jetty Lee, Kaisa Poutanen, Hani El-Nezami

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Oat β-glucan a water soluble non starch linear polysaccharide has been approved as a cholesterol lowering agent by various food safety administrations and is commonly used to reduce the risk of heart disease. The molecular weight of oat β-glucan can vary depending on the extraction and fractionation methods. It is not clear whether the molecular weight has a significant impact at reducing the acceleration of atherosclerosis. The aim of this study was to investigate three different oat β-glucan fractionations on the development of atherosclerosis in vivo. With special focus on plaque stability and the intestinal barrier function. To test this, ApoE-/- female mice were fed a high fat diet supplemented with oat bran, high molecular weight (HMW) oat β-glucan fractionate and low molecular weight (LMW) oat β-glucan fractionate for 16 weeks. Atherosclerosis risk markers were measured in the plasma, heart and aortic tree. Plaque size was measured in the aortic root and aortic tree. ICAM-1, VCAM-1, E-Selectin, P-Selectin, protein levels were assessed from the aortic tree to determine plaque stability at 16 weeks. The expression of p22phox at the aortic root was evaluated to study the NADPH oxidase complex involved in nitric oxide bioavailability and vascular elasticity. The tight junction proteins E-cadherin and beta-catenin from western blot analyses were analysed as an intestinal barrier function test. Plasma LPS, intestinal D-lactate levels and hepatic FMO gene expression were carried out to confirm whether the compromised intestinal barrier lead to endotoxemia. The oat bran and HMW oat β-glucan diet groups were more effective than the LMW β-glucan diet group at reducing the plaque size and showed marked improvements in plaque stability. The intestinal barrier was compromised for all the experimental groups however the endotoxemia levels were higher in the LMW β-glucan diet group. The oat bran and HMW oat β-glucan diet groups were more effective at attenuating the development of atherosclerosis. Reasons for this could be due to the LMW oat β-glucan diet group’s low viscosity in the gut and the inability to block the reabsorption of cholesterol. Furthermore the low viscosity may allow more bacterial endotoxin translocation through the impaired intestinal barrier. In future food technologists should carefully consider how to incorporate LMW oat β-glucan as a health promoting food.

Keywords: Atherosclerosis, beta glucan, endotoxemia, intestinal barrier function

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Authors: Reem Alajmi, Hind Al Harbi, Tahany Ayaad, Zainab Al Musawi

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Hard ticks Hyalomma spp. (family: Ixodidae) are obligate ectoparasite in their all life stages on some domestic animals mainly camels and cattle. Ticks may lead to many economic and public health problems because of their blood feeding behavior. Also, they act as vectors for many bacterial, viral and protozoan agents which may cause serious diseases such as tick-born encephalitis, Rocky-mountain spotted fever, Q-fever and Lyme disease which can affect human and/or animals. In the present study, molecular identification of ticks that attack camels in Riyadh region, Saudi Arabia based on the partial sequence of mitochondrial 16s rRNA gene was applied. Also, the present study aims to detect natural infections of collected camel ticks with Rickessia spp. and Borelia spp. using PCR/hybridization of Citrate synthase encoding gene present in bacterial cells. Hard ticks infesting camels were collected from different camels located in a farm in Riyadh region, Saudi Arabia. Results of the present study showed that the collected specimens belong to two species: Hyalomma dromedari represent 99% of the identified specimens and Hyalomma marginatum which account for 1 % of identified ticks. The molecular identification was made through blasting the obtained sequence of this study with sequences already present and identified in GeneBank. All obtained sequences of H. dromedarii specimens showed 97-100% identity with the same gene sequence of the same species (Accession # L34306.1) which was used as a reference. Meanwhile, no intraspecific variations of H. marginatum mesured because only one specimen was collected. Results also had shown that the intraspecific variability between individuals of H. dromedarii obtained in 92 % of samples ranging from 0.2- 6.6%, while the remaining 7 % of the total samples of H. dromedarii showed about 10.3 % individual differences. However, the interspecific variability between H. dromedarii and H. marginatum was approximately 18.3 %. On the other hand, by using the technique of PCR/hybridization, we could detect natural infection of camel ticks with Rickettsia spp. and Borrelia spp. Results revealed the natural presence of both bacteria in collected ticks. Rickettsial spp. infection present in 29% of collected ticks, while 35% of collected specimen were infected with Borrelia spp. The valuable results obtained from the present study are a new record for the molecular identification of camel ticks in Riyadh, Saudi Arabia and their natural infection with both Rickettsia spp. and Borrelia spp. These results may help scientists to provide a good and direct control strategy of ticks in order to protect one of the most important economic animals which are camels. Also results of this project spotlight on the disease that might be transmitted by ticks to put out a direct protective plan to prevent spreading of these dangerous agents. Further molecular studies are needed to confirm the results of the present study by using other mitochondrial and nuclear genes for tick identification.

Keywords: Camel ticks, Rickessia spp. , Borelia spp. , mitochondrial 16s rRNA gene

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Authors: N. Harun, E. E. Masiren, W. H. W. Ibrahim, F. Adam

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Amine absorption process is an approach for mitigation of CO2 from flue gas that produces from power plant. This process is the most common system used in chemical and oil industries for gas purification to remove acid gases. On the challenges of this process is high energy requirement for solvent regeneration to release CO2. In the past few years, mixed alkanolamines have received increasing attention. In most cases, the mixtures contain N-methyldiethanolamine (MDEA) as the base amine with the addition of one or two more reactive amines such as PZ. The reason for the application of such blend amine is to take advantage of high reaction rate of CO2 with the activator combined with the advantages of the low heat of regeneration of MDEA. Several experimental and simulation studies have been undertaken to understand this process using blend MDEA/PZ solvent. Despite those studies, the mechanism of CO2 absorption into the aqueous MDEA is not well understood and available knowledge within the open literature is limited. The aim of this study is to investigate the intermolecular interaction of the blend MDEA/PZ using Molecular Dynamics (MD) simulation. MD simulation was run under condition 313K and 1 atm using NVE ensemble at 200ps and NVT ensemble at 1ns. The results were interpreted in term of Radial Distribution Function (RDF) analysis through two system of interest i.e binary and tertiary. The binary system will explain the interaction between amine and water molecule while tertiary system used to determine the interaction between the amine and CO2 molecule. For the binary system, it was observed that the –OH group of MDEA is more attracted to water molecule compared to –NH group of MDEA. The –OH group of MDEA can form the hydrogen bond with water that will assist the solubility of MDEA in water. The intermolecular interaction probability of –OH and –NH group of MDEA with CO2 in blended MDEA/PZ is higher than using single MDEA. This findings show that PZ molecule act as an activator to promote the intermolecular interaction between MDEA and CO2.Thus, blend of MDEA with PZ is expecting to increase the absorption rate of CO2 and reduce the heat regeneration requirement.

Keywords: amine absorption process, blend MDEA/PZ, CO2 capture, molecular dynamic simulation, radial distribution function

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Authors: Yasmina Houda Bendahma, Tewfik Bouchaour, Meriem Merad, Ulrich Maschke

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The purpose of this work is to study retention of dye dissolved in distilled water, by an hydrophilic acrylic polymer network. The polymer network considered is Poly (2-hydroxyethyl methacrylate) (PHEMA): it is prepared by photo-polymerization under UV irradiation in the presence of a monomer (HEMA), initiator and an agent cross-linker. PHEMA polymer network obtained can be used in the retention of dye molecules present in the wastewater. The results obtained are interesting in the study of the kinetics of swelling and de-swelling of cross linked polymer networks PHEMA in colored aqueous solutions. The dyes used for retention by the PHEMA networks are eosin Y and Malachite Green, dissolved in distilled water. Theoretical conformational study by a simplified molecular model of system cross linked PHEMA / dye (eosin Y and Malachite Green), is used to simulate the retention phenomenon (or Docking) dye molecules in cavities in nano-domains included in the PHEMA polymer network.

Keywords: dye retention, molecular modeling, photochemically crosslinked polymer network, swelling deswelling, PHEMA, HEMA

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Abas Mohsenzadeh, Tariq Bashir, Waseen Tahir, Ulf Stigh, Mikael Skrifvars, Kim Bolton

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The area of artificial muscles has received significant attention from many research domains including soft robotics, biomechanics and smart textiles in recent years. Poly(vinylidene fluoride) (PVDF) has been used to form artificial muscles since it contracts upon heating when under load. In this study, PVDF fibers were produced by melt spinning technique at different solid state draw ratios and then actuation mechanism for PVDF tie molecules within the semicrystalline region of PVDF polymer has been investigated using molecular dynamics simulations. Tie molecules are polymer chains that link two (or more) crystalline regions in semicrystalline polymers. The changes in fiber length upon heating have been investigated using a novel simulation technique. The results show that conformational changes of the tie molecules from the longer all-trans conformation at low temperature (β structure) to the shorter conformation (α structure) at higher temperature accrue by increasing the temperature. These results may be applied to understand the actuation observed for PVDF upon heating.

Keywords: poly(vinylidene fluoride), molecular dynamics, simulation, actuators, tie molecules, semicrystalline

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Authors: Iram Batool, Aamer Saeed, Irfan Zia Qureshi, Ayesha Razzaq, Saima Kalsoom

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Heterocyclic compounds analogues and their derivatives have attracted strong interest in medicinal chemistry due to their biological and pharmacological properties. A series of new thiazolopyrimidine carboxylates were conveniently synthesized by one-pot three-component reaction of ethyl acetoacetate, 2-aminothiazole and benzaldehyde substituted with electron-donating and electron-withdrawing groups in order to find some more potent antidiabetic and antibacterial drugs. The structures of synthesized compounds were characterized by elemental analysis, IR, 1H NMR, 13C NMR spectroscopy. An in vitro antidiabetic effect was evaluated in adult male BALB/c mice and antibacterial activities were tested against Micrococcus luteus, Salmonella typhimurium, Bacillus subtilis, Bordetella bronchiseptica and Escherichia coli. Some of the tested compounds proved to possess good to excellent activities more than the reference drugs. An in silico molecular docking was also performed on synthesized compounds. The current study is expected to provide useful insights into the design of antidiabetic and antibacterial drugs and understanding the mechanism by which such drugs interact with RNA and diabetes target and exert their biochemical action.

Keywords: antidiabetic, antibacterial, MOE docking, thiazolopyrimidine

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Authors: Drashti G. Daraji, Rosa E. Moo-Puc, Hitesh D. Patel

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Substituted 2-Thioimidazole analogues have been synthesized and confirmed by advanced spectroscopic techniques. Among them, ten compounds have been selected and evaluated for their in vitro anti-cancer activity at the National Cancer Institute (NCI) for testing against a panel of 60 different human tumor cell lines derived from nine neoplastic cancer types. Furthermore, synthesized compounds were tested for their in vitro antiprotozoal activity, and none of them exhibited significant potency against antiprotozoans. It was observed that the tested all compounds seem effective on the UACC-62 melanoma cancer cell line as compared to other cancer cell lines and also exhibited the least potent in the Non-Small Cell Lung Cancer cell line in one-dose screening. In silico studies of these derivatives were carried out by molecular docking techniques and Absorption, Distribution, Metabolism, and Excretion (ADME) using Schrödinger software to find potent B-Raf kinase inhibitor (PDB ID: 3OG7). All the compounds have been performed for docking study; Compound D4 has a good docking score for melanoma cancer as compared with other.

Keywords: anticancer activity, cancer cell line, 2-thio imidazole, one-dose assay, molecular docking

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Authors: Ertuğ Yıldırım, Dile Kara, Salih Zeki Yıldız

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Metal containing polymers (MCPs) are macro molecules usually containing metal-ligand coordination units and are a multidisciplinary research field mainly based at the interface between coordination chemistry and polymer science. The progress of this area has also been reinforced by the growth of several other closely related disciplines including macro molecular engineering, crystal engineering, organic synthesis, supra molecular chemistry and colloidal and material science. Schiff base ligands are very effective in constructing supra molecular architectures such as coordination polymers, double helical and triple helical complexes. In addition, Schiff base derivatives incorporating a fluorescent moiety are appealing tools for optical sensing of metal ions. MCPs are well-known systems in which the combinations of local parameters are possible by means of fluoro metric techniques. Generally, without incorporation of the fluorescent groups with polymers is unspecific, and it is not useful to analyze their fluorescent properties. Therefore, it is necessary to prepare a new type epoxy polymers with fluorescent groups in terms of metal sensing prop and the other photo chemical applications. In the present study metal containing polymers were prepared via poly functional monomeric Schiff base metal chelate complexes in the presence of dis functional monomers such as diglycidyl ether Bisphenol A (DGEBA). The synthesized complexes and polymers were characterized by FTIR, UV-VIS and mass spectroscopies. The preparations of epoxy polymers have been carried out at 185 °C. The prepared composites having sharp and narrow excitation/emission properties are expected to be applicable in various systems such as heat-resistant polymers and photo voltaic devices. The prepared composite is also ideal for various applications, easily prepared, safe, and maintain good fluorescence properties.

Keywords: Schiff base ligands, crystal engineering, fluorescence properties, Metal Containing Polymers (MCPs)

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Authors: K. Żak, S. Przetocka, R. Kitel, K. Guzik, B. Musielak, S. Malicki, G. Dubin, T. A. Holak

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Studies on tumor genesis revealed a number of factors that may potentially serve as molecular targets for immunotherapies. One of such promising targets are PD1 and PDL1 proteins. PD1 (Programmed cell death protein 1) is expressed by activated T cells and plays a critical role in modulation of the host's immune response. One of the PD1 ligands -PDL1- is expressed by macrophages, monocytes and cancer cells which exploit it to avoid immune attack. The notion of the mechanisms used by cancer cells to block the immune system response was utilized in the development of therapies blocking PD1-PDL1 interaction. Up to date, human PD1-PDL1 complex has not been crystallized and structure of the mouse-human complex does not provide a complete view of the molecular basis of PD1-PDL1 interactions. The purpose of this study is to obtain crystal structure of the human PD1-PDL1 complex which shall allow rational design of small molecule inhibitors of the interaction. In addition, the study presents results of binding small-molecules to PD1 and fragment docking towards PD1 protein which will facilitate the design and development of small–molecule inhibitors of PD1-PDL1 interaction.

Keywords: PD1, PDL1, cancer, small molecule, drug discovery

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Authors: Beverley Gallimore

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The Individuals with Disabilities Education Act of 2004 (IDEA) has helped to improve outcomes for students with special education needs. Through IDEA, students with Special Education Needs (SEN) have opportunities for more equitable education within the General Education classroom. However, students with disabilities lack access to instructions that can help them to maximize their fullest learning potential. Recently, educational stakeholders have emphasized Integrated Co-teaching as a tool to increase engagement and learning outcomes for students with disabilities in general education classrooms. As a result of this new approach, general and special education teachers are working collaboratively to teach students with disabilities. However, co-teaching models are not properly designed and structured to effectively benefit students with disabilities. Teachers must be oriented correctly in the co-teaching models if it is to be beneficial for students.

Keywords: CO-teaching, differentiation, equitable, collaborative

Procedia PDF Downloads 60

Authors: H. K. Ratre, M. Roy, S. Roy, M. S. Parmar, V. Bhagat

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Mastitis is a common problem of dairy industries. Reduction in milk production and an irreparable damage to the udder associated with the disease are common causes of culling of dairy cows. Milk from infected animals is not suitable for drinking and for making different milk products. So, it has a major economic importance in dairy cattle. The aims of this study were to investigate the bacteriological panorama in milk from udder quarters with subclinical mastitis and to carried out for the molecular characterization of the major isolated organisms, from subclinical mastitis-affected cows in and around Durg and Rajnandgaon district of Chhattisgarh. Isolation and identification of bacteria from the milk samples of subclinical mastitis-affected cows were done by standard and routine culture procedures. A total of 78 isolates were obtained from cows and among the various bacteria isolated, Staphylococcus spp. occupied prime position with occurrence rate of 51.282%. However, other bacteria isolated includeStreptococcus spp. (20.512%), Micrococcus spp. (14.102%), E. coli (8.974%), Klebsiela spp. (2.564%), Salmonella spp. (1.282%) and Proteus spp. (1.282%). Staphylococcus spp. was isolated as the major causative agent of subclinical mastitis in the studied area. Molecular characterization of Staphylococus aureusisolates was done for genetic expression of the virulence genes like ‘nuc’ encoding thermonucleaseexoenzyme, coa and spa by PCR amplification of the respective genes in 25 Staphylococcus isolates. In the present study, 15 isolates (77.27%) out of 20 coagulase positive isolates were found to be genotypically positive for ‘nuc’ where as 20 isolates (52.63%) out of 38 CNS expressed the presence of the same virulence gene. In the present study, three Staphylococcus isolates were found to be genotypically positive for coa gene. The Amplification of the coa gene yielded two different products of 627, 710 bp. The amplification of the gene segment encoding the IgG binding region of protein A (spa) revealed a size of 220 and 253bp in twostaphylococcus isolates. The X-region binding of the spa gene produced an amplicon of 315 bp in one Staphylococcal isolates. Staphylococcus aureus was found to be major isolate (51.28%) responsible for causing subclinical mastitis in cows which also showed expression of virulence genesnuc, coa and spa.

Keywords: mastitis, bacteria, characterization, expression, gene

Procedia PDF Downloads 196

Authors: Jiahui Song

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The use of electric fields with high intensity (~ 100kV/cm or higher) and ultra short pulse durations (nanosecond range) has been a recent development. Most of the studies of electroporation have ignored possible thermal effects because of the small duration of the applied voltage pulses. However, it has been predicted membrane temperature gradients ranging from 0.2×109 to 109 K/m. This research focuses on thermal effects that drive for electroporative enhancements, even though the actual temperature values might not have changed appreciably from their equilibrium levels. The dynamics of pore formation with the application of an externally applied electric field is studied on the basis of molecular dynamics (MD) simulations using the GROMACS package. MD simulations of a lipid layer with constant electric field strength of 0.5 V/nm at 25 °C and 47 °C are implemented to simulate the appropriate thermal effects. The GROMACS provides the force fields for the lipid membranes, which is taken to comprise of dipalmitoyl-phosphatidyl-choline (DPPC) molecules. The water model mimicks the aqueous environment surrounding the membrane. Velocities of water and membrane molecules are generated randomly at each simulation run according to a Maxwellian distribution. The high background electric field is typically used in MD simulations to probe electroporation. It serves as an accelerated test of the pore formation process since low electric fields would take inordinately long simulation time. MD simulation shows no pore is formed in a 1-ns snapshot for a DPPC membrane set at a temperature of 25°C after a 0.5 V/nm electric field is applied. A nano-sized pore is clearly seen in a 0.75-ns snapshot on the same geometry, but with the membrane surfaces kept at temperatures of 47°C. And the pore increases at 1 ns. The MD simulation results suggest the possibility that the increase in temperature can result in different degrees of electrically stimulated bio-effects. The results points to the role of thermal effects in facilitating and accelerating the electroporation process.

Keywords: high-intensity, ultra-short, electroporation, thermal effects, molecular dynamics

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Authors: Fakhrosadat Sajjadian, Ramin Ghasemi Shayan

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The tumor microenvironment plays an fundamental part in tumor start, movement, metastasis, and treatment resistance. It varies from ordinary tissue in terms of its extracellular network, vascular and lymphatic arrange, as well as physiological conditions. The clinical application of atomic cancer imaging is regularly prevented by the tall commercialization costs of focused on imaging operators as well as the constrained clinical applications and little showcase measure of a few operators. . Since numerous cancer types share comparable characteristics of the tumor microenvironment, the capacity to target these biomarkers has the potential to supply clinically translatable atomic imaging advances for numerous types encompassing cancer and broad clinical applications. Noteworthy advance has been made in focusing on the tumor microenvironment for atomic cancer imaging. In this survey, we summarize the standards and methodologies of later progresses in atomic imaging of the tumor microenvironment, utilizing distinctive imaging modalities for early discovery and conclusion of cancer. To conclude, The tumor microenvironment (TME) encompassing tumor cells could be a profoundly energetic and heterogeneous composition of safe cells, fibroblasts, forerunner cells, endothelial cells, flagging atoms and extracellular network (ECM) components.

Keywords: molecular, imaging, TME, medicine

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Authors: Sorin Muraru

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Computational generation of carbon nanostructures is still a very demanding process. This work provides an alternative to manual molecular modeling through an algorithm meant to automate the design of such structures. Specifically, carbon nanochimneys are obtained through the bonding of a carbon nanotube with the smaller edge of an open carbon nanocone. The methods of connection rely on mathematical, geometrical and chemical properties. Non-hexagonal rings are used in order to perform the correct bonding of dangling bonds. Once obtained, they are useful for thermal transport, gas storage or other applications such as gas separation. The carbon nanochimneys are meant to produce a less steep connection between structures such as the carbon nanotube and graphene sheet, as in the pillared graphene, but can also provide functionality on its own. The method relies on connecting dangling bonds at the edges of the two carbon nanostructures, employing the use of two different types of auxiliary structures on a case-by-case basis. The code is implemented in Python 3.7 and generates an output file in the .pdb format containing all the system’s coordinates. Acknowledgment: This work was supported by a grant of the Executive Agency for Higher Education, Research, Development and innovation funding (UEFISCDI), project number PN-III-P1-1.1-TE-2016-24-2, contract TE 122/2018.

Keywords: carbon nanochimneys, computational, carbon nanotube, carbon nanocone, molecular modeling, carbon nanostructures

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Authors: Jamileh Ahmed, Helena Hernandez, Gabriel De Erausquin

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H1N1 virus susceptibility of iPSC-derived DA neurons from schizophrenia patients and controls will compared. C57/BL-6 fibroblasts were reprogrammed into iPSCs using a lenti-viral vector containing SOKM genes. Pluripotency verification with the AP assay and immunocytochemistry ensured iPSC presence. The experimental outcome of ISPCs from DA neuron differentiation will be discussed in the Results section. Fibroblasts from patients and controls will be reprogrammed into iPSCs using a sendai-virus vector containing SOKM. IPSCs will be characterized using the AP assay, immunocytochemistry and RT-PCR. IPSCs will then be differentiated into DA neurons. Gene methylation will be compared for both groups with custom-designed microarrays.

Keywords: schizophrenia, iPSCs, stem cells, neuroscience

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Authors: Lokesh Soni, Sushanta Kumar Sethi, Gaurav Manik

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This work attempts to use molecular simulations to create equilibrated structures of a range of commercially used polymers. Generated equilibrated structures for polyvinyl acetate (isotactic), polyvinyl alcohol (atactic), polystyrene, polyethylene, polyamide 66, poly dimethyl siloxane, poly carbonate, poly ethylene oxide, poly amide 12, natural rubber, poly urethane, and polycarbonate (bisphenol-A) and poly ethylene terephthalate are employed to estimate the correct chain length that will correctly predict the chain parameters and properties. Further, the equilibrated structures are used to predict some properties like density, solubility parameter, cohesive energy density, surface energy, and Flory-Huggins interaction parameter. The simulated densities for polyvinyl acetate, polyvinyl alcohol, polystyrene, polypropylene, and polycarbonate are 1.15 g/cm3, 1.125 g/cm3, 1.02 g/cm3, 0.84 g/cm3 and 1.223 g/cm3 respectively are found to be in good agreement with the available literature estimates. However, the critical repeating units or the degree of polymerization after which the solubility parameter showed saturation were 15, 20, 25, 10 and 20 respectively. This also indicates that such properties that dictate the miscibility of two or more polymers in their blends are strongly dependent on the chosen polymer or its characteristic properties. An attempt has been made to correlate such properties with polymer properties like Kuhn length, free volume and the energy term which plays a vital role in predicting the mentioned properties. These results help us to screen and propose a useful library which may be used by the research groups in estimating the polymer properties using the molecular simulations of chains with the predicted critical lengths. The library shall help to obviate the need for researchers to spend efforts in finding the critical chain length needed for simulating the mentioned polymer properties.

Keywords: Kuhn length, Flory Huggins interaction parameter, cohesive energy density, free volume

Procedia PDF Downloads 179