Search results for: cellular and molecular mechanism

Authors: Emma K. Sales, Nilda G. Butardo

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The project was undertaken to determine the effects of modified tissue culture protocols e.g. age of culture and hormone levels (2,4-D) in generating somaclonal variation. Moreover, the utility of molecular markers (SSR and MSAP) in sorting off types/somaclones were investigated. Results show that somaclonal variation is in effect due to prolonged subculture and high 2,4-D concentration. The resultant variation was observed to be due to high level of methylation events specifically cytosine methylation either at the internal or external cytosine and was identified by methylation sensitive amplification polymorphism (MSAP). Simple sequence repeats (SSR) on the other hand, was able to associate a marker to a trait of interest. These therefore, show that molecular markers can be an important tool in sorting out variation/mutants at an early stage.

Keywords: methylation, MSAP, somaclones, SSR, subculture, 2, 4-D

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Authors: Kyung-Tae Lee, Li Li Wang, Kwang-Woo Jung, Yong-Sun Bahn

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Microtubules are involved in mechanical support, cytoplasmic organization as well as in a number of cellular processes by interacting with diverse microtubule-associated proteins (MAPs), such as plus-end tracking proteins, motor proteins, and tubulin-folding cofactors. A common feature of these proteins is the presence of a cytoskeleton-associated protein-glycine-rich (CAP-Gly) domain, which is evolutionarily conserved and generally considered to bind to α-tubulin to regulate functions of microtubules. However, there has been a dearth of research on CAP-Gly proteins in fungal pathogens, including Cryptococcus neoformans, which causes fatal meningoencephalitis globally. In this study, we identified five CAP-Gly proteins encoding genes in C. neoformans. Among these, Cgp1, encoded by CNAG_06352, has a unique domain structure that has not been reported before in other eukaryotes. Supporting the role of Cpg1 in microtubule-related functions, we demonstrate that deletion or overexpression of CGP1 alters cellular susceptibility to thiabendazole, a microtubule destabilizer, and Cgp1 is co-localized with cytoplasmic microtubules. Related to the cellular functions of microtubules, Cgp1 also governs maintenance of membrane stability and genotoxic stress responses. Furthermore, we demonstrate that Cgp1 uniquely regulates sexual differentiation of C. neoformans with distinct roles in the early and late stage of mating. Our domain analysis reveals that the CAP-Gly domain plays major roles in all the functions of Cgp1. Finally, the cgp1Δ mutant is attenuated in virulence. In conclusion, this novel CAP-Gly protein, Cgp1, has pleotropic roles in regulating growth, stress responses, differentiation and pathogenicity of C. neoformans.

Keywords: human fungal pathogen, CAP-Glycine protein, microtubule, meningoencephalitis

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: synthetic gene network, network identification, optimization, nonlinear modeling

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Authors: Sumayah Mohammed Asiri A., Aviva Levina B., Elizabeth New C., Peter Lay D.

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Pt compounds have been among the most successful anticancer drugs in the last 40 years, but the development of resistance to them is an increasing problem. Cellular homeostasis of an essential metal, Cu, is known to be involved in Pt resistance, but mechanisms of this process are poorly understood. We used a novel ratiometric Cu(I)-sensitive fluorescent probeInCCu1 dye to detect Cu(I) in the mitochondria. Total Cu and labile Cu pool measured using AAS and InCCu1 dye in A2780 cells and their corresponding resistant cells A2780-cis.R cells treated with Cu and cisplatin. The main difference between both cell lines in the presence and absence of Cu(II) is that resistant cells have lower total Cu content but higher labile Cu levels than cisplatin-sensitive cells. This means that resistant cells can metabolize and export excess Cu more efficiently. Furthermore, InCCu1 has emerged not only as an indicator of labile cellular Cu levels in the mitochondria but as a potentially versatile multi-organelle probe.

Keywords: AAS and ICPMS, A2780 and its resistant cells, ratiometric fluorescent sensors, inCCu1, and total and labile Cu

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Authors: Sara Torabi, Sadegh Khazalpour, Mahdi Jamshidi

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Nitro aromatic compounds are valuable materials because of their applications in the preparation of chemical intermediates for the synthesis of dyes, plastics, perfumes, energetic materials, and pharmaceuticals. Chemical and electrochemical procedures are reported for nitration of aromatic compounds. Flavonoid derivatives are present in many vegetables and fruits and are constituent of many common pharmaceuticals and dietary supplements. Electrochemistry provides very versatile means for the electrosynthesis, mechanistic and kinetic studies. To the best of our knowledge, and despite the importance of these compounds in numerous scientific fields, there are no reports on the electrochemical nitration of Quercetin derivatives. Herein, we describe a green electrochemical synthesis of a nitro compound. In this work, electrochemical oxidation of Quercetin has been studied in the presence of nitrite ion as a nucleophile in acetate buffer solution (c = 0.2 M, pH = 6.0), by means of cyclic voltammetry and controlled-potential coulometry. The results indicate the participation of produced o-benzoquinones in Michael reaction with nitrite ion (in the divided cell) to form the corresponding nitro diol (EC mechanism). The purity of product and characterization was done using ¹H NMR, ¹³C NMR, FTIR spectroscopic techniques. The presented strategies use a water/ethanol mixture as solvent. Ethanol as cosolvent was also used in the previous studies because of its low cost, safety, easy availability, recyclability, bioproductability, and biodegradability. These strategies represent a one-pot and facile process for the synthesis of nitro compound in high yield and purity under green conditions.

Keywords: electrochemical synthesis, green chemistry, cyclic voltammetry, molecular docking

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Authors: Muhammet Baldan, Emel Timuçin

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Generally, absorption and bioavailability increase if solubility increases; therefore, it is crucial to predict them in drug discovery applications. Molecular descriptors and Molecular properties are traditionally used for the prediction of water solubility. There are various key descriptors that are used for this purpose, namely Drogan Descriptors, Morgan Descriptors, Maccs keys, etc., and each has different prediction capabilities with differentiating successes between different data sets. Another source for the prediction of solubility is structural features; they are commonly used for the prediction of solubility. However, there are little to no studies that combine three or more properties or descriptors for prediction to produce a more powerful prediction model. Unlike available models, we used a combination of those features in a random forest machine learning model for improved solubility prediction to better predict and, therefore, contribute to drug discovery systems.

Keywords: solubility, molecular descriptors, machine learning, random forest

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Authors: Z. Bayat

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A quantitative structure–property relationship (QSPR) study was performed to develop models those relate the structures of 65 Kovats retention index (RI) of adamantane derivatives. Molecular descriptors derived solely from 3D structures of the molecular compounds. The usefulness of the quantum chemical descriptors, calculated at the level of the DFT theories using 6-311+G** basis set for QSAR study of adamantane derivatives was examined. The use of descriptors calculated only from molecular structure eliminates the need to experimental determination of properties for use in the correlation and allows for the estimation of RI for molecules not yet synthesized. The prediction results are in good agreement with the experimental value. A multi-parametric equation containing maximum Four descriptors at B3LYP/6-31+G** method with good statistical qualities (R2train=0.913, Ftrain=97.67, R2test=0.770, Ftest=3.21, Q2LOO=0.895, R2adj=0.904, Q2LGO=0.844) was obtained by Multiple Linear Regression using stepwise method.

Keywords: DFT, adamantane, QSAR, Kovat

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Authors: O. H. Gebril, N. A. Meguid

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Background: Iron had been a focus of interest recently as a main exaggerating factor for oxidative stresses in the central nervous system and a link to various neurological disorders is suspected. Many studies with various techniques showed evidence of disturbed iron-related proteins in the cell in human and animal models of neurodegenerative disorders. Also, linkage to significant pathological changes had been evidenced e.g. apoptosis and cell signaling. On the other hand, the role of iron in neurodevelopmental disorders is still unclear. With increasing prevalence of autism worldwide, some changes in iron parameters and its stores were documented in many studies. This study includes Haemochromatosis HFE gene polymorphisms (p.H63D and p.C282Y) and ferroportin gene (SLC40A1) Q248H polymorphism in autism and control children. Materials and Methods: Whole genome DNA was extracted; p.H63D and p.C282Y genotyping was studied using specific sequence amplification followed by restriction enzyme digestion on a sample of autism patients (25 cases) and twenty controls. Results: The p.H63D is seen more than the C282Y among both autism and control samples, with no significant association of p.H63D or p.C282Y polymorphism and autism was revealed. Also, no association with Q248H polymorphism was evidenced. Conclusion: The study results do not prove the role of cellular iron genes polymorphisms as risk factors for neurodevelopmental disorders, and in turn highlights the specificity of cellular iron related pathways in neurodegeneration. These results demand further gene expression studies to elucidate the main pathophysiological pathways that are disturbed in autism and other neurodevelopmental disorders.

Keywords: iron, neurodevelopmental, oxidative stress, haemohromatosis, ferroportin, genes

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Authors: Gizelle K. Vianna, Gustavo S. Oliveira, Gabriel V. Cunha

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The use of decision support systems in agriculture may help monitoring large fields of crops by automatically detecting the symptoms of foliage diseases. In our work, we designed and implemented a decision support system for small tomatoes producers. This work investigates ways to recognize the late blight disease from the analysis of digital images of tomatoes, using a pair of multilayer perceptron neural networks. The networks outputs are used to generate repainted tomato images in which the injuries on the plant are highlighted, and to calculate the damage level of each plant. Those levels are then used to construct a situation map of a farm where a cellular automata simulates the outbreak evolution over the fields. The simulator can test different pesticides actions, helping in the decision on when to start the spraying and in the analysis of losses and gains of each choice of action.

Keywords: artificial neural networks, cellular automata, decision support system, pattern recognition

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Authors: Seyyed Feisal Asbaghian Namin, Reza Pilafkan, Mahmood Kaffash Irzarahimi

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TThis paper considers vibration of single-layered graphene sheets using molecular dynamics (MD) and nonlocal elasticity theory. Based on the MD simulations, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), an open source software, is used to obtain fundamental frequencies. On the other hand, governing equations are derived using nonlocal elasticity and first order shear deformation theory (FSDT) and solved using generalized differential quadrature method (GDQ). The small-scale effect is applied in governing equations of motion by nonlocal parameter. The effect of different side lengths, boundary conditions and nonlocal parameter are inspected for aforementioned methods. Results are obtained from MD simulations is compared with those of the nonlocal elasticity theory to calculate appropriate values for the nonlocal parameter. The nonlocal parameter value is suggested for graphene sheets with various boundary conditions. Furthermore, it is shown that the nonlocal elasticity approach using classical plate theory (CLPT) assumptions overestimates the natural frequencies.

Keywords: graphene sheets, molecular dynamics simulations, fundamental frequencies, nonlocal elasticity theory, nonlocal parameter

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Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

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In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: anti-cancer drug, center of mass, interaction energy, molecular dynamics simulation, nanocarrier

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Authors: Lalita Subedi, Jae Kyoung Chae, Yong Un Park, Cho Kyo Hee, Lee Jae Hyuk, Kang Min Cheol, Sun Yeou Kim

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Neuroinflammation may mediate the relationship between low levels of estrogens and neurodegenerative disease. Estrogens are neuroprotective and anti-inflammatory in neurodegenerative disease models. Due to the long term side effects of estrogens, researches have been focused on finding an effective phytoestrogens for biological activities. Daidzein present in soybeans and its active metabolite equol (7-hydroxy-3-(4'-hydroxyphenyl)-chroman) bears strong antioxidant and anticancer showed more potent anti-inflammatory and neuroprotective role in neuroinflammatory model confirmed its in vitro activity with molecular mechanism through NF-κB pathway. Three major CNS cells Microglia (BV-2), Astrocyte (C6), Neuron (N2a) were used to find the effect of equol in inducible nitric oxide synthase (iNOS), cyclooxygenase (COX-2), MAPKs signaling proteins, apoptosis related proteins by western blot analysis. Nitric oxide (NO) and prostaglandin E2 (PGE2) was measured by the Gries method and ELISA, respectively. Cytokines like tumor necrosis factor-α (TNF-α) and IL-6 were also measured in the conditioned medium of LPS activated cells with or without equol. Equol inhibited the NO production, PGE-2 production and expression of COX-2 and iNOS in LPS-stimulated microglial cells at a dose dependent without any cellular toxicity. At the same time Equol also showed promising effect in modulation of MAPK’s and nuclear factor kappa B (NF-κB) expression with significant inhibition of the production of proinflammatory cytokine like interleukin -6 (IL-6), and tumor necrosis factor -α (TNF-α). Additionally, it inhibited the LPS activated microglia-induced neuronal cell death by downregulating the apoptotic phenomenon in neuronal cells. Furthermore, equol increases the production of neurotrophins like NGF and increase the neurite outgrowth as well. In conclusion the natural daidzein metabolite equol are more active than daidzein, which showed a promising effectiveness as an anti-neuroinflammatory and neuroprotective agent via downregulating the LPS stimulated microglial activation and neuronal apoptosis. This work was supported by Brain Korea 21 Plus project and High Value-added Food Technology Development Program 114006-4, Ministry of Agriculture, Food and Rural Affairs.

Keywords: apoptosis, equol, neuroinflammation, phytoestrogen

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Authors: Sungkyung Kim, Jee-Hyeon Na, Dong-Seung Kwon

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Future mobile networks following 5th generation will be characterized by one thousand times higher gains in capacity; connections for at least one hundred billion devices; user experience capable of extremely low latency and response times. To be close to the capacity requirements and higher reliability, advanced technologies have been studied, such as multiple connectivity, small cell enhancement, heterogeneous networking, and advanced interference and mobility management. This paper is focused on the multiple connectivity in heterogeneous cellular networks. We investigate the performance of coverage and user throughput in several deployment scenarios. Using the stochastic geometry approach, the SINR distributions and the coverage probabilities are derived in case of dual connection. Also, to compare the user throughput enhancement among the deployment scenarios, we calculate the spectral efficiency and discuss our results.

Keywords: heterogeneous networks, multiple connectivity, small cell enhancement, stochastic geometry

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Authors: Jiahui Song

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In order to predict or explain a complicated biological process, it is important first to construct mathematical models that can be used to yield analytical solutions. Through numerical simulation, mathematical model results can be used to test scenarios that might not be easily attained in a laboratory experiment, or to predict parameters or phenomena. High-intensity, nanosecond pulse electroporation has been a recent development in bioelectrics. The dynamic pore model can be achieved by including a dynamic aspect and a dependence on the pore population density into pore formation energy equation to analyze and predict such electroporation effects. For greater accuracy, with inclusion of atomistic details, molecular dynamics (MD) simulations were also carried out during this study. Besides inducing pores in cells, external voltages could also be used in principle to modulate action potential generation in nerves. This could have an application in electrically controlled ‘pain management’. Also a simple model-based rate equation treatment of the various cellular bio-chemical processes has been used to predict the pulse number dependent cell survival trends.

Keywords: model, high-intensity, nanosecond, bioelectrics

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Authors: H. V. H. De Soysa, N. D. Hiripitiya, H. S. U. Thrimavithana, B. R. Epitawala, K. A. D. D. Kuruppu, D. J. K. Lokupathirage

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This research was based on developing a mechanism in order to optimize the landing distance. Short distance braking and long distance braking may cause several issues for the aircraft including tyre wearing. The worst case occurs with short distance landing. The issues related to short distance landing were identified after conducting interviews with pilots, aeronautical engineers and technicians. A model was constructed in order to optimize the landing distance. The device started to function at the point where the main wheels of the aircraft touchdown the runway. It was found that implementing this device to the aircraft benefits to optimize the landing distance. This could lead to rectifying several issues occurred due to improper braking distances.

Keywords: aircraft, mechanism, optimize landing distance, runway

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Authors: Saeed Alzahrani, Yaser Miaji

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The project involves the design and simulation of a Mobile Cellular Telecommunication Network using the software tool CelPlanner. The design is mainly concerned with Global System for Mobile Communications . The design and simulation of the network is done for a small part of the area allocated for us in the terrain area of Shreveport city .The project is concerned with designing a network that is cost effective and which also efficiently meets the required Grade of Service (GOS) AND Quality of Service (QOS).The expected outcome of this project is the design of a network that gives a good coverage for the area allocated to us with minimum co-channel interference and adjacent channel interference. The Handover and Traffic Handling Capacity should also be taken into consideration and should be good for the given area . The Traffic Handling Capacity of the network in a way decides whether the designed network is good or bad . The design also takes into consideration the topographical and morphological information.

Keywords: mobile communication, GSM, radio base station, network planning

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Authors: Vinod Nair, C. Sadasivan

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Beta-lactam antibiotics are the most frequently prescribed medications in modern medicine. The antibiotic resistance by the production of enzyme beta-lactamase is an important mechanism seen in microorganisms. Resistance to beta-lactams mediated by beta-lactamases can be overcome successfully with the use of beta-lactamase inhibitors. New generations of the antibiotics contain mostly synthetic compounds, and many side effects have been reported for them. Combinations of beta-lactam and beta-lactamase inhibitors have become one of the most successful antimicrobial strategies in the current scenario of bacterial infections. Plant-based drugs are very cheap and having lesser adverse effect than synthetic compounds. The synergistic effect of eugenol acetate with beta-lactams restores the activity of beta-lactams, allowing their continued clinical use. It is reported here the enhanced inhibitory effect of phytochemical, eugenol acetate, isolated from the plant Syzygium aromaticum with beta-lactams on beta-lactamase. The compound was found to have synergistic effect with the antibiotic amoxicillin against antibiotic-resistant strain of S.aureus. The enzyme was purified from the organism and incubated with the compound. The assay showed that the compound could inhibit the enzymatic activity of beta-lactamase. Modeling and molecular docking studies indicated that the compound can fit into the active site of beta-lactamase and can mask the important residue for hydrolysis of beta-lactams. The synergistic effects of eugenol acetate with beta-lactam antibiotics may justify, the use of these plant compounds for the preparation of β-lactamase inhibitors against β-lactam resistant S.aureus.

Keywords: betalactamase, eugenol acetate, synergistic effect, molecular modeling

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Authors: Hanjun Zhao, Ke Zhang, Bojian Zheng

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Background: So far, there is no universal antiviral agent which can inhibit multiple viral infections. More and more drug-resistant viral strains emerge after the antiviral drug application for treatment. Defensins are the front line of host innate immunity and have broad spectrum antibacterial and antiviral effects. However, there is limited data to show if these defensins have good antiviral activity in vivo and what the antiviral mechanism is. Subjects: To investigate a peptide with widespread antivirus activity in vitro and in vivo and illustrate the antiviral mechanism. Methods: Antiviral peptide library designed from mouse beta defensins was synthesized by the company. Recombinant beta defensin was obtained from E. coli. Antiviral activity in vitro was assayed by plaque assay, qPCR. Antiviral activity in vivo was detected by animal challenge with 2009 pandemic H1N1 influenza A virus. The antiviral mechanism was assayed by western blot, ELISA, and qPCR. Conclusions: We identify a new peptide which has widespread effects against multiple viruses (H1N1, H5N1, H7N9, MERS-CoV) in vitro and has efficient antivirus activity in vivo. This peptide inhibits viral entry into target cells and subsequently blocks viral replication. The in vivo study of the antiviral peptide against other viral infections and the investigation of its more detail antiviral mechanism are ongoing.

Keywords: antiviral peptide, defensin, Influenza A virus, mechanism

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Authors: Han Xiao, Zhang Lei, Huang Hai, Lv Shizeng

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Space environment simulator is a device for spacecraft test. KM8 large space environment simulator built in Tianjing Space City is the largest as well as the most advanced space environment simulator in China. Large deviation of spacecraft level will lead to abnormally work of the thermal control device in spacecraft during the thermal vacuum test. In order to avoid thermal vacuum test failure, level adjusting mechanism system is developed in the KM8 large space environment simulator as one of the most important subsystems. According to the level adjusting requirements of spacecraft’s thermal vacuum tests, the four fulcrums adjusting model is established. By means of collecting level instruments and displacement sensors data, stepping motors controlled by PLC drive four supporting legs simultaneous movement. In addition, a PID algorithm is used to control the temperature of supporting legs and level instruments which long time work under the vacuum cold and black environment in KM8 large space environment simulator during thermal vacuum tests. Based on the above methods, the data acquisition and processing, the analysis and calculation, real time adjustment and fault alarming of the level adjusting mechanism system are implemented. The level adjusting accuracy reaches 1mm/m, and carrying capacity is 20 tons. Debugging showed that the level adjusting mechanism system of KM8 large space environment simulator can meet the thermal vacuum test requirement of the new generation spacecraft. The performance and technical indicators of the level adjusting mechanism system which provides important support for the development of spacecraft in China have been ahead of similar equipment in the world.

Keywords: space environment simulator, thermal vacuum test, level adjusting, spacecraft, parallel mechanism

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Authors: Ewelina Nowak, Anna Wisla-Swider, Krzysztof Danel

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Aqueous suspensions of DNA were illuminated with linearly polarized visible light and ultraviolet for 5, 15, 20 and 40 h. In order to check the nature of modification, DNA interactions were characterized by FTIR spectroscopy. For each illuminated sample, weight average molecular weight and hydrodynamic radius were measured by high pressure size exclusion chromatography. Resulting optical changes for illuminated DNA were investigated using UV-Vis spectra and photoluminescent. Optical properties show potential application in sensors based on modified DNA. Then selected DNA-surfactant complexes were illuminated with electromagnetic radiation for 5h. Molecular structure, optical characteristic were examinated for obtained complexes. Illumination led to changes of complexes physicochemical properties as compared with native DNA. Observed changes were induced by rearrangement of the molecular structure of DNA chains.

Keywords: biopolymers, deoxyribonucleic acid, ionic liquids, linearly polarized visible light, ultraviolet

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Authors: F. S. Irwansyah, I. Farida, Y. Maulana

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Studying chemistry requires the ability to understand three levels of understanding in the form of macroscopic, submicroscopic and symbolic, but the lack of emphasis on the submicroscopic level leads to the understanding of chemical concepts becoming incomplete, due to the limitations of the tools capable of providing visualization of submicroscopic concepts. The purpose of this study describes the stages of making augmented reality learning media on the concept of molecular geometry and analyze the feasibility test result of augmented reality learning media on the concept of molecular geometry. This research uses Research and Development (R & D) method which produces a product of AR learning media on molecular geometry concept and test the effectiveness of the product. Research stages include concept analysis and learning indicators, design development, validation, feasibility, and limited testing. The stages of validation and limited trial are aimed to get feedback in the form of assessment, suggestion and improvement on learning aspect, material substance aspect, visual communication aspect and software engineering aspects and media feasibility in terms of media creation purpose to be used in learning. The results of the overall feasibility test obtained r-calculation 0,7-0,9 with the interpretation of high feasibility value, whereas the result of limited trial got the percentage of eligibility with the average value equal to 70,83-92,5%. This percentage indicates that AR's learning media product on the concept of molecular geometry, deserves to be used as a learning resource.

Keywords: android, augmented reality, chemical learning, geometry

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Authors: Abdul Majid, Alia Jabeen, Nimra Zulifqar

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The inorganic molecular crystal (IMCs) due to their unusual structure has grabbed a lot of attention due to anisotropy in crystal structure. The IMCs consist of the molecular structures joined together via weak forces. Therefore, a difference between the bonding between the inter-cage and intra-cage interactions exists. To look closely at the bonding and interactions, we investigated interactions between two cages of Sb2O3 structure. The interactions were characterized via Extended Transition State-Natural Orbital for Chemical Valence-method (ETS-NOCV), Natural Bond Orbitals (NBO) and Quantum Theory of Atoms in Molecules (QTAIM). The results revealed strong intra-cage covalent bonding while weak van der Waals (vdWs) interactions along inter-cages exits. This structure cannot be termed as layered material although they have anisotropy in bonding and presence of weak vdWs interactions but its bulk is termed as inorganic layered clusters. This is due to the fact that the free standing sheet/films with these materials are not possible. This type of structures may be the most feasible to be used for the system to deal with high pressures and stress bearing materials.

Keywords: inorganic molecular crystals, density functional theory, cages, interactions

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Authors: Peter Egri, Tamas Kis

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Scheduling problems have been studied by the algorithmic mechanism design research from the beginning. This paper is focusing on a practically important, but theoretically rather neglected field: the project scheduling problem where the jobs connected by precedence constraints compete for various nonrenewable resources, such as materials. Although the centralized problem can be solved in polynomial-time by applying the algorithm of Carlier and Rinnooy Kan from the Eighties, obtaining materials in a decentralized environment is usually far from optimal. It can be observed in practical production scheduling situations that project managers tend to cache the required materials as soon as possible in order to avoid later delays due to material shortages. This greedy practice usually leads both to excess stocks for some projects and materials, and simultaneously, to shortages for others. The aim of this study is to develop a model for the material allocation problem of a production plant, where a central decision maker—the inventory—should assign the resources arriving at different points in time to the jobs. Since the actual due dates are not known by the inventory, the mechanism design approach is applied with the projects as the self-interested agents. The goal of the mechanism is to elicit the required information and allocate the available materials such that it minimizes the maximal tardiness among the projects. It is assumed that except the due dates, the inventory is familiar with every other parameters of the problem. A further requirement is that due to practical considerations monetary transfer is not allowed. Therefore a mechanism without money is sought which excludes some widely applied solutions such as the Vickrey–Clarke–Groves scheme. In this work, a type of Serial Dictatorship Mechanism (SDM) is presented for the studied problem, including a polynomial-time algorithm for computing the material allocation. The resulted mechanism is both truthful and Pareto optimal. Thus the randomization over the possible priority orderings of the projects results in a universally truthful and Pareto optimal randomized mechanism. However, it is shown that in contrast to problems like the many-to-many matching market, not every Pareto optimal solution can be generated with an SDM. In addition, no performance guarantee can be given compared to the optimal solution, therefore this approximation characteristic is investigated with experimental study. All in all, the current work studies a practically relevant scheduling problem and presents a novel truthful material allocation mechanism which eliminates the potential benefit of the greedy behavior that negatively influences the outcome. The resulted allocation is also shown to be Pareto optimal, which is the most widely used criteria describing a necessary condition for a reasonable solution.

Keywords: material allocation, mechanism without money, polynomial-time mechanism, project scheduling

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Authors: Harika Atmaca, Emir Bozkurt, Latife Merve Oktay, Selim Uzunoglu, Ruchan Uslu, Burçak Karaca

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Microarrays have been developed for highly parallel enzyme-linked immunosorbent assay (ELISA) applications. The most common protein arrays are produced by using multiple monoclonal antibodies, since they are robust molecules which can be easily handled and immobilized by standard procedures without loss of activity. Protein expression profiling with protein array technology allows simultaneous analysis of the protein expression pattern of a large number of proteins. Trabectedin, a tetrahydroisoquinoline alkaloid derived from a Caribbean tunicate, Ecteinascidia turbinata, has been shown to have antitumor effects. Here, we used a novel proteomic approach to explore the mechanism of action of trabectedin in prostate cancer cell line PC-3 by apoptosis antibody microarray. XTT cell proliferation kit and Cell Death Detection Elisa Plus Kit (Roche) was used for measuring cytotoxicity and apoptosis. Human Apoptosis Protein Array (R&D Systems) which consists of 35 apoptosis related proteins was used to assess the omic protein expression pattern. Trabectedin induced cytotoxicity and apoptosis in prostate cancer cells in a time and concentration-dependent manner. The expression levels of the death receptor pathway molecules, TRAIL-R1/DR4, TRAIL R2/DR5, TNF R1/TNFRSF1A, FADD were significantly increased by 4.0-, 21.0-, 4.20- and 11.5-fold by trabectedin treatment in PC-3 cells. Moreover, mitochondrial pathway related pro-apoptotic proteins Bax, Bad, Cytochrome c, and Cleaved Caspase-3 expressions were induced by 2.68-, 2.07-, 2.8-, and 4.5-fold and the expression levels of anti-apoptotic proteins Bcl-2 and Bcl-XL were reduced by 3.5- and 5.2-fold in PC-3 cells. Proteomic (antibody microarray) analysis suggests that the mechanism of action of trabectedin may be exerted via the induction of both intrinsic and extrinsic apoptotic pathways. The antibody microarray platform can be utilised to explore the molecular mechanism of action of novel anticancer agents.

Keywords: trabectedin, prostate cancer, omic protein expression profile, apoptosis

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Authors: Tsu-Hsu Yen

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The interfacial gas adsorption presents a frequent challenge and opportunity for micro-/nano-fluidic operation. In this study, we investigate the wettability, gas accumulation, and nanobubble formation on various homogeneous surface conditions by using MD simulation, including a series of 3D and quasi-2D argon-water-solid systems simulation. To precisely determine the wettability on various substrates, several indicators were calculated. Among these wettability indicators, the water PMF (potential of mean force) has the most correlation tendency with interfacial water molecular orientation than depletion layer width and droplet contact angle. The results reveal that the aggregation of argon molecules on substrates not only depending on the level of hydrophobicity but also determined by the competition between gas-solid and water-solid interaction as well as water molecular structure near the surface. In addition, the surface nanobubble is always observed coexisted with the gas enrichment layer. The water structure adjacent to water-gas and water-solid interfaces also plays an important factor in gas out-flux and gas aggregation, respectively. The quasi-2D simulation shows that only a slight difference in the curved argon-water interface from the plane interface which suggests no noticeable obstructing effect on gas outflux from the gas-water interfacial water networks.

Keywords: gas aggregation, interfacial nanobubble, molecular dynamics simulation, wettability

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Authors: Amit Chaudhary, B. S. Yadav, P. K. Maurya, A. M., S. Srivastava, S. Singh, A. Mani

Abstract:

Cold shock protein A (CspA) is major cold inducible protein present in Escherichia coli. The protein is involved in stabilizing secondary structure of RNA by working as chaperone during cold temperature. Two RNA binding motifs play key role in the stabilizing activity. This study aimed to investigate implications of low temperature on structure and RNA binding activity of E. coli CspA. Molecular dynamics simulations were performed to compare the stability of the protein at 37°C and 10 °C. The protein was mutated at RNA binding motifs and docked with RNA to assess the stability of both complexes. Results suggest that CspA as well as CspA-RNA complex is more stable at low temperature. It was also confirmed that RNP1 and RNP2 play key role in RNA binding.

Keywords: CspA, homology modelling, mutation, molecular dynamics simulation

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Authors: Mahesh Pal, Tripti Mishra, Chandana Rao, Dalip Upreti

Abstract:

Cancer has been considered to be a very dreadful disease. Holmskioldia sanguinea is a large climbing shrub found in the Himalayas at an altitude of 5,000 ft and preliminary investigation showed the excellent yield of andrographolide and subjected for the anticancer activity. Protective effect of Holmskioldia sanguinea leaf ethanolic extract has been investigated against Ehrlich ascites carcinoma (EAC) and Daltons ascites lymphoma (DAL) in Swiss albino mice to evaluate the possible mechanism of action. The enzymatic antioxidant status was studied on tumor bearing mice, which shows the potential of the compound to possess significant free radical scavenging property and revealed significant tumor regression and prolonged survival time. The isolated bioactive molecule andrographolide from Holmskioldia sanguinea yields (2.5%) in subject to HPTLC/HPLC analysis. The cellular defense system constituting the superoxide dismutase, catalyses was enhanced whereby the lipid peroxidation content was restricted to a larger extent. The Holmskioldia sanguinea is a new source of andrographolide and demonstrated the potency in treatment of cancer.

Keywords: Holmskioldia sanguinea, tumor, mice, andrographolide

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Authors: Tanima Chatterjee, Maitree Bhattacharyya

Abstract:

The global challenge of type 2 diabetes mellitus is a major health concern in this millennium, and researchers are continuously exploring new targets to develop a novel therapeutic strategy. Type 2 diabetes mellitus (T2DM) is often coupled with dyslipidemia increasing the risks for cardiovascular (CVD) complications. Enhanced oxidative and nitrosative stresses appear to be the major risk factors underlying insulin resistance, dyslipidemia, β-cell dysfunction, and T2DM pathogenesis. Autophagy emerges to be a promising defense mechanism against stress-mediated cell damage regulating tissue homeostasis, cellular quality control, and energy production, promoting cell survival. In this study, we have attempted to explore the pivotal role of autophagy in T2DM subjects with or without dyslipidemia in peripheral blood mononuclear cells and insulin-resistant HepG2 cells utilizing flow cytometric platform, confocal microscopy, and molecular biology techniques like western blotting, immunofluorescence, and real-time polymerase chain reaction. In the case of T2DM with dyslipidemia higher population of autophagy, positive cells were detected compared to patients with the only T2DM, which might have resulted due to higher stress. Autophagy was observed to be triggered both by oxidative and nitrosative stress revealing a novel finding of our research. LC3 puncta was observed in peripheral blood mononuclear cells and periphery of HepG2 cells in the case of the diabetic and diabetic-dyslipidemic conditions. Increased expression of ATG5, LC3B, and Beclin supports the autophagic pathway in both PBMC and insulin-resistant Hep G2 cells. Upon blocking autophagy by 3-methyl adenine (3MA), the apoptotic cell population increased significantly, as observed by caspase‐3 cleavage and reduced expression of Bcl2. Autophagy has also been evidenced to control oxidative stress-mediated up-regulation of inflammatory markers like IL-6 and TNF-α. To conclude, this study elucidates autophagy to play a protective role in the case of diabetes mellitus with dyslipidemia. In the present scenario, this study demands to have a significant impact on developing a new therapeutic strategy for diabetic dyslipidemic subjects by enhancing autophagic activity.

Keywords: autophagy, apoptosis, dyslipidemia, reactive oxygen species, reactive nitrogen species, Type 2 diabetes

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Authors: S. Cheragh Dar, M. Saljooghi, A. Babrgir

Abstract:

In the last couple of decades researchers' attitudes were focused on developing and enhancing heat transfer processes by using new components or cellular solids that divide into stochastic structures and periodic structures. Open-cell metal foams are part of stochastic structures families that they can be considered as an avant-garde technology and they have unique properties, this porous media can have tremendous achievements in thermal processes. This paper argues and surveys postulating possible in industrial thermal issues which include: compact electronic cooling, heat exchanger, aerospace, fines, turbo machinery, automobiles, crygen tanks, biomechanics, high temperature filters and etc. Recently, by surveying exponential rate of publications in thermal open-cell metal foams, all can be demonstrated in a holistic view which can lead researchers to a new level of understanding in different industrial thermal sections.

Keywords: heat transfer, industrial thermal, cellular solids, open cell metal foam

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Authors: Irlana C. do Mar, Thayna A. Ferreira, Dayane S. Rezende, Bruno A. M. Figueira, José M. R. Mercury

Abstract:

This work presents a low-cost Mn starting material to synthesis manganese oxide octahedral molecular sieve with Mg²⁺ in the tunnel (Mg-OMS-1), based on the Mn residues from Carajás Mineral Province (Amazon, Brazil). After hydrothermal and cation exchange procedures, the Mn residues transformed to a single phase, Mg-OMS-1. The raw material and the synthesis processes were analyzed by means of X-ray diffraction (XRD), Scanning electron microscopy (SEM) and Infrared spectroscopy (FTIR). The tunnel structure was synthesized hydrothermally at 180 °C for three days without impurities. According to the XRD analysis, the formation of crystalline Mg-OMS-1 was identified through reflections at 9.8º, 12º and 18º (2θ), as well as a thermal stability around 300 ºC. The SEM analysis indicated that the final product presents good crystallinity with a homogeneous size. In addition, an intense and diagnostic FTIR band was identified at 515 cm⁻¹ related to the MnO₆ octahedral stretching vibrations.

Keywords: Mn residues , Octahedral Molecular Sieve, Synthesis, Characterization

Procedia PDF Downloads 172