Search results for: molecular%20docking

Authors: Yan Ren, Fei Guo, Jun Qiao, Shengwei Hu, Hui Zhang, Yuanzhi Wang, Pengyan Wang, Jinliang Sheng, Xinli Gu, Xiaojun Liu, Chuangfu Chen

Abstract:

Bovine viral diarrhea virus (BVDV) can cause lifelong persistent infection. One reason for the phenomena is attributed to BVDV infection to placenta tissue. However the mechanisms that BVDV invades into placenta tissue remain unclear. To clarify the molecular mechanisms, we investigated the possible means that BVDV entered into bovine trophoblast cells (TPC). Yeast two-hybrid system was used to identify proteins extracted from TPC, which interact with BVDV envelope glycoprotein E2. A PGbkt7-E2 yeast expression vector and TPC cDNA library were constructed. Through two rounds of screening, three positive clones were identified. Sequencing analysis indicated that all the three positive clones encoded the same protein clathrin. Physical interaction between clathrin and BVDV E2 protein was further confirmed by coimmunoprecipitation experiments. This result suggested that the clathrin might play a critical role in the process of BVDV entry into placenta tissue and might be a novel antiviral target for preventing BVDV infection.

Keywords: Bovine viral diarrhea virus, clathrin, glycoprotein E2, yeast two-hybrid system.

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Authors: I.Banerjee, A.K.Mahendra, T.K.Bera, B.G.Chandresh

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The scroll pump belongs to the category of positive displacement pump can be used for continuous pumping of gases at low pressure apart from general vacuum application. The shape of volume occupied by the gas moves and deforms continuously as the spiral orbits. To capture flow features in such domain where mesh deformation varies with time in a complicated manner, mesh less solver was found to be very useful. Least Squares Kinetic Upwind Method (LSKUM) is a kinetic theory based mesh free Euler solver working on arbitrary distribution of points. Here upwind is enforced in molecular level based on kinetic flux vector splitting scheme (KFVS). In the present study we extended the LSKUM to moving node viscous flow application. This new code LSKUM-NS-MN for moving node viscous flow is validated for standard airfoil pitching test case. Simulation performed for flow through scroll pump using LSKUM-NS-MN code agrees well with the experimental pumping speed data.

Keywords: Least Squares, Moving node, Pitching, Spirals.

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Authors: Amaneh Javid, Shahin Ahmadian, Ali A. Saboury, Saeed Rezaei-Zarchi

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This study determines the effect of naked and heparinbased super-paramagnetic iron oxide nanoparticles on the human cancer cell lines of A2780. Doxorubicin was used as the anticancer drug, entrapped in the SPIO-NPs. This study aimed to decorate nanoparticles with heparin, a molecular ligand for 'active' targeting of cancerous cells and the application of modified-nanoparticles in cancer treatment. The nanoparticles containing the anticancer drug DOX were prepared by a solvent evaporation and emulsification cross-linking method. The physicochemical properties of the nanoparticles were characterized by various techniques, and uniform nanoparticles with an average particle size of 110±15 nm with high encapsulation efficiencies (EE) were obtained. Additionally, a sustained release of DOX from the SPIO-NPs was successful. Cytotoxicity tests showed that the SPIO-DOX-HP had higher cell toxicity than the individual HP and confocal microscopy analysis confirmed excellent cellular uptake efficiency. These results indicate that HP based SPIO-NPs have potential uses as anticancer drug carriers and also have an enhanced anticancer effect.

Keywords: Heparin, A2780 cells, ovarian cancer, nanoparticles, doxorubicin.

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Authors: Noor Zainab Habib, Ibrahim Kamaruddin, Madzalan Napiah, Isa Mohd Tan

Abstract:

This paper presents a part of research on the rheological properties of bitumen modified by thermoplastic namely linear low density polyethylene (LLDPE), high density polyethylene (HDPE) and polypropylene (PP) and its interaction with 80 pen base bitumen. As it is known that the modification of bitumen by the use of polymers enhances its performance characteristics but at the same time significantly alters its rheological properties. The rheological study of polymer modified bitumen (PMB) was made through penetration, ring & ball softening point and viscosity test. The results were then related to the changes in the rheological properties of polymer modified bitumen. It was observed that thermoplastic copolymer shows profound effect on penetration rather than softening point. The viscoelastic behavior of polymer modified bitumen depend on the concentration of polymer, mixing temperature, mixing technique, solvating power of base bitumen and molecular structure of polymer used. PP offer better blend in comparison to HDPE and LLDPE. The viscosity of base bitumen was also enhanced with the addition of polymer. The pseudoplastic behavior was more prominent for HDPE and LLDPE than PP. Best results were obtained when polymer concentration was kept below 3%

Keywords: Polymer modified bitumen, Linear low densitypolyethylene, High density polyethylene, Polypropylene.

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Authors: A. Ghaffari, A. S. Mostafavi

Abstract:

Complex assemblies of interacting proteins carry out most of the interesting jobs in a cell, such as metabolism, DNA synthesis, mitosis and cell division. These physiological properties play out as a subtle molecular dance, choreographed by underlying regulatory networks that control the activities of cyclin-dependent kinases (CDK). The network can be modeled by a set of nonlinear differential equations and its behavior predicted by numerical simulation. In this paper, an innovative approach has been proposed that uses genetic algorithms to mine a set of behavior data output by a biological system in order to determine the kinetic parameters of the system. In our approach, the machine learning method is integrated with the framework of existent biological information in a wiring diagram so that its findings are expressed in a form of system dynamic behavior. By numerical simulations it has been illustrated that the model is consistent with experiments and successfully shown that such application of genetic algorithms will highly improve the performance of mathematical model of the cell division cycle to simulate such a complicated bio-system.

Keywords: Cell cycle, Cyclin-dependent kinase, Fission yeast, Genetic algorithms, Mathematical modeling, Wiring diagram

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Authors: Hasmik P. Ter-Voskanyan

Abstract:

The account of genus Polygonum L. in "Flora of Armenia" was made more than five decades ago. After that many expeditions have been carried out in different regions of Armenia and a huge herbarium material has been collected. The genus included 5 sections with 20 species. Since then many authors accepted the sections as separate genera on the basis of anatomical, morphological, palynological and molecular data. According to the above mentioned it became clear, that the taxonomy of Armenian representatives of Polygonum s. l. also needs revision. New literature data and our investigations of live and herbarium material (ERE, LE) with specification of the morphological characters, distribution, ecology, flowering and fruiting terms brought us to conclusion, that genus Polygonum s. l. has to be split into 5 different genera (Aconogonon (Meisn.) Reichenb., Bistorta (L.) Scop., Fallopia Adans., Persicaria Mill., Polygonum L. s. s.). The number of species has been reduced to 16 species. For each genus new determination keys has been created. 

Keywords: Aconogonon (Meisn.) Reichenb., Bistorta (L.) Scop., Fallopia Adans., Persicaria Mill., Polygonum L. s. s., Flora of Armenia.

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Authors: Bianca Schweiger, Lucile Bahnweg, Barbara Palm, Ute Steinfeld

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The occurrence and removal of trace organic contaminants in the aquatic environment has become a focus of environmental concern. For the selective removal of carbamazepine from loaded waters molecularly imprinted polymers (MIPs) were synthesized with carbamazepine as template. Parameters varied were the type of monomer, crosslinker, and porogen, the ratio of starting materials, and the synthesis temperature. Best results were obtained with a template to crosslinker ratio of 1:20, toluene as porogen, and methacrylic acid (MAA) as monomer. MIPs were then capable to recover carbamazepine by 93% from a 10-5 M landfill leachate solution containing also caffeine and salicylic acid. By comparison, carbamazepine recoveries of 75% were achieved using a nonimprinted polymer (NIP) synthesized under the same conditions, but without template. In landfill leachate containing solutions carbamazepine was adsorbed by 93-96% compared with an uptake of 73% by activated carbon. The best solvent for desorption was acetonitrile, with which the amount of solvent necessary and dilution with water was tested. Selected MIPs were tested for their reusability and showed good results for at least five cycles. Adsorption isotherms were prepared with carbamazepine solutions in the concentration range of 0.01 M to 5*10-6 M. The heterogeneity index showed a more homogenous binding site distribution.

Keywords: Carbamazepine, landfill leachate, removal, reuse

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Authors: Fabian Horn, Reinhard Guthke

Abstract:

In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.

Keywords: bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection

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Authors: Eggertson, E.C. Kapulla, R, Fokken, J, Prasser, H.M.

Abstract:

The turbulent mixing of coolant streams of different temperature and density can cause severe temperature fluctuations in piping systems in nuclear reactors. In certain periodic contraction cycles these conditions lead to thermal fatigue. The resulting aging effect prompts investigation in how the mixing of flows over a sharp temperature/density interface evolves. To study the fundamental turbulent mixing phenomena in the presence of density gradients, isokinetic (shear-free) mixing experiments are performed in a square channel with Reynolds numbers ranging from 2-500 to 60-000. Sucrose is used to create the density difference. A Wire Mesh Sensor (WMS) is used to determine the concentration map of the flow in the cross section. The mean interface width as a function of velocity, density difference and distance from the mixing point are analyzed based on traditional methods chosen for the purposes of atmospheric/oceanic stratification analyses. A definition of the mixing layer thickness more appropriate to thermal fatigue and based on mixedness is devised. This definition shows that the thermal fatigue risk assessed using simple mixing layer growth can be misleading and why an approach that separates the effects of large scale (turbulent) and small scale (molecular) mixing is necessary.

Keywords: Concentration measurements, Mixedness, Stablystratified turbulent isokinetic mixing layer, Wire mesh sensor

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Authors: H. Djaara, M. Yahia, H. Bousselsela, N Khelif, A. Zidani, S. Benbia.

Abstract:

Von Willebrand-s disease is the most common inherited bleeding disorder in humans, it caused by qualitative abnormalities of the von Willebrand factor (vWF). Our objective is to determine the prevalence of this disease at part of the Algerian population in the East and the South by a biological diagnosis based on specific biological tests (automated platelet count, the bleeding time (TS), the time of cephalin + activator (TCA), measure of the prothrombin rate (TP), vWF rate and factor VIII rate, Molecular electrophoresis of vWF multimers in agarose gel in the presence of SDS). Four patients of type III or severe Willebrand-s disease were found on 200 suspect cases. All cases are showed a deficit in vWF rate (< 5%), and factor VIII (P<0, 0001), and lengthening very significantly high of the TCA (P<0, 0001) and of the bleeding time (P<0,0001), with a normal blood platelet rate (P=0,7433) and a normal prothrombin rate (P=0,5808), an absence of all the multimers of vWF in plasma patients. The severe Willebrand-s disease is not only one pathology of primary haemostasis, but it can be accompanied by coagulation-s anomaly due to deficit in factor VIII. At this studied population, von Willebrand-s disease is less frequent (2%) than other hemorrhagic syndromes identified by the differential diagnosis like the thrombocytopenia (36%).

Keywords: Von Willebrand's disease, differential diagnosis, von Willebrand factor, factor VIII, biological diagnosis, thrombocytopenia.

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Authors: N. H. Abd Raof, H. Abu Hassan, S.K. Mohd Bakhori, S. S. Ng, Z. Hassan

Abstract:

Quaternary InxAlyGa1-x-yN semiconductors have attracted much research interest because the use of this quaternary offer the great flexibility in tailoring their band gap profile while maintaining their lattice-matching and structural integrity. The structural and optical properties of InxAlyGa1-x-yN alloys grown by molecular beam epitaxy (MBE) is presented. The structural quality of InxAlyGa1-x-yN layers was characterized using high-resolution X-ray diffraction (HRXRD). The results confirm that the InxAlyGa1-x-yN films had wurtzite structure and without phase separation. As the In composition increases, the Bragg angle of the (0002) InxAlyGa1-x-yN peak gradually decreases, indicating the increase in the lattice constant c of the alloys. FWHM of (0002) InxAlyGa1-x-yN decreases with increasing In composition from 0 to 0.04, that could indicate the decrease of quality of the samples due to point defects leading to non-uniformity of the epilayers. UV-VIS spectroscopy have been used to study the energy band gap of InxAlyGa1-x-yN. As the indium (In) compositions increases, the energy band gap decreases. However, for InxAlyGa1-x-yN with In composition of 0.1, the band gap shows a sudden increase in energy. This is probably due to local alloy compositional fluctuations in the epilayer. The bowing parameter which appears also to be very sensitive on In content is investigated and obtained b = 50.08 for quaternary InxAlyGa1-x-yN alloys. From photoluminescence (PL) measurement, green luminescence (GL) appears at PL spectrum of InxAlyGa1-x-yN, emitted for all x at ~530 nm and it become more pronounced as the In composition (x) increased, which is believed cause by gallium vacancies and related to isolated native defects.

Keywords: HRXRD, nitrides, PL, quaternary, UV-VIS.

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Authors: P. Kowalska, P. Gabka, K. Kamieniarz, M. Kamieniarz, W. Stryla, P. Guzik, T. Krauze

Abstract:

We have developed a computer program consisting of 6 subtests assessing the children hand dexterity applicable in the rehabilitation medicine. We have carried out a normative study on a representative sample of 285 children aged from 7 to 15 (mean age 11.3) and we have proposed clinical standards for three age groups (7-9, 9-11, 12-15 years). We have shown statistical significance of differences among the corresponding mean values of the task time completion. We have also found a strong correlation between the task time completion and the age of the subjects, as well as we have performed the test-retest reliability checks in the sample of 84 children, giving the high values of the Pearson coefficients for the dominant and non-dominant hand in the range 0.740.97 and 0.620.93, respectively. A new MATLAB-based programming tool aiming at analysis of cardiologic RR intervals and blood pressure descriptors, is worked out, too. For each set of data, ten different parameters are extracted: 2 in time domain, 4 in frequency domain and 4 in Poincaré plot analysis. In addition twelve different parameters of baroreflex sensitivity are calculated. All these data sets can be visualized in time domain together with their power spectra and Poincaré plots. If available, the respiratory oscillation curves can be also plotted for comparison. Another application processes biological data obtained from BLAST analysis.

Keywords: Biomedical data base processing, Computer software, Hand dexterity, Heart rate and blood pressure variability.

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Authors: Ratnakar Tripathi, Rajnikant Mishra

Abstract:

The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.

Keywords: Interacting Proteins, Pax6, PIP, STRING

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Authors: Sarkar M. A. Kawsar, Sarkar M. A. Mamun, Md S. Rahman, Hidetaro Yasumitsu, Yasuhiro Ozeki

Abstract:

Lectins have a good scope in current clinical microbiology research. In the present study evaluated the antimicrobial activities of a D-galactose binding lectin (PnL) was purified from the annelid, Perinereis nuntia (polychaeta) by affinity chromatography. The molecular mass of the lectin was determined to be 32 kDa as a single polypeptide by SDS-PAGE under both reducing and non-reducing conditions. The hemagglutinating activity of the PnL showed against trypsinized and glutaraldehyde-fixed human erythrocytes was specifically inhibited by D-Gal, GalNAc, Galβ1-4Glc and Galα1-6Glc. PnL was evaluated for in vitro antibacterial screening studies against 11 gram-positive and gram-negative microorganisms. From the screening results, it was revealed that PnL exhibited significant antibacterial activity against gram-positive bacteria. Bacillus megaterium showed the highest growth inhibition by the lectin (250 μg/disc). However, PnL did not inhibit the growth of gram-negative bacteria such as Vibrio cholerae and Pseudomonas sp. PnL was also examined for in vitro antifungal activity against six fungal phytopathogens. PnL (100 μg/mL) inhibited the mycelial growth of Alternaria alternata (24.4%). These results indicate that future findings of lectin applications obtained from annelids may be of importance to life sciences.

Keywords: Perinereis nuntia, Lectin, Inhibition zone, Mycelial growth.

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Authors: M. W. Lau, C. O. Ng

Abstract:

This is a study on numerical simulation of the convection-diffusion transport of a chemical species in steady flow through a small-diameter tube, which is lined with a very thin layer made up of retentive and absorptive materials. The species may be subject to a first-order kinetic reversible phase exchange with the wall material and irreversible absorption into the tube wall. Owing to the velocity shear across the tube section, the chemical species may spread out axially along the tube at a rate much larger than that given by the molecular diffusion; this process is known as dispersion. While the long-time dispersion behavior, well described by the Taylor model, has been extensively studied in the literature, the early development of the dispersion process is by contrast much less investigated. By early development, that means a span of time, after the release of the chemical into the flow, that is shorter than or comparable to the diffusion time scale across the tube section. To understand the early development of the dispersion, the governing equations along with the reactive boundary conditions are solved numerically using the Flux Corrected Transport Algorithm (FCTA). The computation has enabled us to investigate the combined effects on the early development of the dispersion coefficient due to the reversible and irreversible wall reactions. One of the results is shown that the dispersion coefficient may approach its steady-state limit in a short time under the following conditions: (i) a high value of Damkohler number (say Da ≥ 10); (ii) a small but non-zero value of absorption rate (say Γ* ≤ 0.5).

Keywords: Dispersion coefficient, early development of dispersion, FCTA, wall reactions.

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Authors: Sayyed R Mousavi

Abstract:

The Far From Most Strings Problem (FFMSP) is to obtain a string which is far from as many as possible of a given set of strings. All the input and the output strings are of the same length, and two strings are said to be far if their hamming distance is greater than or equal to a given positive integer. FFMSP belongs to the class of sequences consensus problems which have applications in molecular biology. The problem is NP-hard; it does not admit a constant-ratio approximation either, unless P = NP. Therefore, in addition to exact and approximate algorithms, (meta)heuristic algorithms have been proposed for the problem in recent years. On the other hand, in the recent years, hybrid algorithms have been proposed and successfully used for many hard problems in a variety of domains. In this paper, a new metaheuristic algorithm, called Constructive Beam and Local Search (CBLS), is investigated for the problem, which is a hybridization of constructive beam search and local search algorithms. More specifically, the proposed algorithm consists of two phases, the first phase is to obtain several candidate solutions via the constructive beam search and the second phase is to apply local search to the candidate solutions obtained by the first phase. The best solution found is returned as the final solution to the problem. The proposed algorithm is also similar to memetic algorithms in the sense that both use local search to further improve individual solutions. The CBLS algorithm is compared with the most recent published algorithm for the problem, GRASP, with significantly positive results; the improvement is by order of magnitudes in most cases.

Keywords: Bioinformatics, Far From Most Strings Problem, Hybrid metaheuristics, Matheuristics, Sequences consensus problems.

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Authors: Sarkar M. A. Kawsar, Sarkar M. A. Mamun, Md S. Rahman, Hidetaro Yasumitsu, Yasuhiro Ozeki

Abstract:

The present study has been taken to explore the screening of in vitro antimicrobial activities of D-galactose-binding sponge lectin (HOL-30). HOL-30 was purified from the marine demosponge Halichondria okadai by affinity chromatography. The molecular mass of the lectin was determined to be 30 kDa with a single polypeptide by SDS-PAGE under non-reducing and reducing conditions. HOL-30 agglutinated trypsinized and glutaraldehydefixed rabbit and human erythrocytes with preference for type O erythrocytes. The lectin was subjected to evaluation for inhibition of microbial growth by the disc diffusion method against eleven human pathogenic gram-positive and gram-negative bacteria. The lectin exhibited strong antibacterial activity against gram-positive bacteria, such as Bacillus megaterium and Bacillus subtilis. However, it did not affect against gram-negative bacteria such as Salmonella typhi and Escherichia coli. The largest zone of inhibition was recorded of Bacillus megaterium (12 in diameter) and Bacillus subtilis (10 mm in diameter) at a concentration of the lectin (250 μg/disc). On the other hand, the antifungal activity of the lectin was investigated against six phytopathogenic fungi based on food poisoning technique. The lectin has shown maximum inhibition (22.83%) of mycelial growth of Botrydiplodia theobromae at a concentration of 100 μg/mL media. These findings indicate that the lectin may be of importance to clinical microbiology and have therapeutic applications.

Keywords: Antibacterial, Halichondria okadai, Inhibition zone, Lectin.

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Authors: Fereshteh Shacheraghi, Mohammad Reza Shakibaie, Hanieh Noveiri

Abstract:

Fourty one strains of ESBL producing P.aeruginosa which were previously isolated from burn patients in Kerman University general hospital, Iran were subjected to PCR, RFLP and sequencing in order to determine the type of extended spectrum β- lactamases (ESBL), the restriction digestion pattern and possibility of mutation among detected genes. DNA extraction was carried out by phenol chloroform method. PCR for detection of bla genes was performed using specific primer for each gene. Restriction Fragment Length Polymorphism (RFLP) for ESBL genes was carried out using EcoRI, NheI, PVUII, EcoRV, DdeI, and PstI restriction enzymes. The PCR products were subjected to direct sequencing of both the strands for identification of the ESBL genes.The blaCTX-M, blaVEB-1, blaPER-1, blaGES-1, blaOXA-1, blaOXA-4 and blaOXA-10 genes were detected in the (n=1) 2.43%, (n=41)100%, (n=28) 68.3%, (n=10) 24.4%, (n=29) 70.7%, (n=7)17.1% and (n=38) 92.7% of the ESBL producing isolates respectively. The RFLP analysis showed that each ESBL gene has identical pattern of digestion among the isolated strains. Sequencing of the ESBL genes confirmed the genuinety of PCR products and revealed no mutation in the restriction sites of the above genes. From results of the present investigation it can be concluded that blaVEB-1 and blaCTX-M were the most and the least frequently isolated ESBL genes among the P.aeruginosa strains isolated from burn patients. The RFLP and sequencing analysis revealed that same clone of the bla genes were indeed existed among the antibiotic resistant strains.

Keywords: ESBL genes, PCR, RFLP, Sequencing, P.aeruginosa

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Authors: Paola Lecca

Abstract:

Modeling and simulation of biochemical reactions is of great interest in the context of system biology. The central dogma of this re-emerging area states that it is system dynamics and organizing principles of complex biological phenomena that give rise to functioning and function of cells. Cell functions, such as growth, division, differentiation and apoptosis are temporal processes, that can be understood if they are treated as dynamic systems. System biology focuses on an understanding of functional activity from a system-wide perspective and, consequently, it is defined by two hey questions: (i) how do the components within a cell interact, so as to bring about its structure and functioning? (ii) How do cells interact, so as to develop and maintain higher levels of organization and functions? In recent years, wet-lab biologists embraced mathematical modeling and simulation as two essential means toward answering the above questions. The credo of dynamics system theory is that the behavior of a biological system is given by the temporal evolution of its state. Our understanding of the time behavior of a biological system can be measured by the extent to which a simulation mimics the real behavior of that system. Deviations of a simulation indicate either limitations or errors in our knowledge. The aim of this paper is to summarize and review the main conceptual frameworks in which models of biochemical networks can be developed. In particular, we review the stochastic molecular modelling approaches, by reporting the principal conceptualizations suggested by A. A. Markov, P. Langevin, A. Fokker, M. Planck, D. T. Gillespie, N. G. van Kampfen, and recently by D. Wilkinson, O. Wolkenhauer, P. S. Jöberg and by the author.

Keywords: Mathematical structure, algorithmic implementation, biochemical network models.

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Authors: Is Fatimah, Winda Novita, Yopi Andika, Imam Sahroni, Basitoh Djaelani, Yuyun Yunani N.

Abstract:

Contamination of aromatic compounds in water can cause severe long-lasting effects not only for biotic organism but also on human health. Several alternative technologies for remediation of polluted water have been attempted. One of these is adsorption process of aromatic compounds by using organic modified clay mineral. Porous structure of clay is potential properties for molecular adsorptivity and it can be increased by immobilizing hydrophobic structure to attract organic compounds. In this work natural montmorillonite were modified with cetyltrimethylammonium (CTMA+) and was evaluated for use as adsorbents of aromatic compounds: benzene, toluene, and 2-chloro phenol in its single and multicomponent solution by ethanol:water solvent. Preparation of CTMA-montmorillonite was conducted by simple ion exchange procedure and characterization was conducted by using x-day diffraction (XRD), Fourier-transform infra red (FTIR) and gas sorption analysis. The influence of structural modification of montmorillonite on its adsorption capacity and adsorption affinity of organic compound were studied. It was shown that adsorptivity of montmorillonite was increased by modification associated with arrangements of CTMA+ in the structure even the specific surface area of modified montmorillonite was lower than raw montmorillonite. Adsorption rate indicated that material has affinity to adsorb compound by following order: benzene> toluene > 2-chloro phenol. The adsorption isotherms of benzene and toluene showed 1st order adsorption kinetic indicating a partition phenomenon of compounds between the aqueous and organophilic CTMAmontmorillonite.

Keywords: Adsorption, Desorption, Montmorillonite, Organoclay, Surfactant.

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Authors: Phannee Saengkaew, Weerasak Ussawawongaraya, Sasiphan Khaweerat, Supagorn Rugmai, Sirisart Ouajai, Jiraporn Luengviriya, Sakuntam Sanorpim, Manop Tirarattanasompot, Somboon Rhianphumikarakit

Abstract:

We present a preliminary x-ray study on human-hair microstructures for a health-state indicator, in particular a cancer case. As an uncomplicated and low-cost method of x-ray technique, the human-hair microstructure was analyzed by wide-angle x-ray diffractions (XRD) and small-angle x-ray scattering (SAXS). The XRD measurements exhibited the simply reflections at the d-spacing of 28 Å, 9.4 Å and 4.4 Å representing to the periodic distance of the protein matrix of the human-hair macrofibrous and the diameter and the repeated spacing of the polypeptide alpha helixes of the photofibrils of the human-hair microfibrous, respectively. When compared to the normal cases, the unhealthy cases including to the breast- and ovarian-cancer cases obtained higher normalized ratios of the x-ray diffracting peaks of 9.4 Å and 4.4 Å. This likely resulted from the varied distributions of microstructures by a molecular alteration. As an elemental analysis by x-ray fluorescence (XRF), the normalized quantitative ratios of zinc(Zn)/calcium(Ca) and iron(Fe)/calcium(Ca) were determined. Analogously, both Zn/Ca and Fe/Ca ratios of the unhealthy cases were obtained higher than both of the normal cases were. Combining the structural analysis by XRD measurements and the elemental analysis by XRF measurements exhibited that the modified fibrous microstructures of hair samples were in relation to their altered elemental compositions. Therefore, these microstructural and elemental analyses of hair samples will be benefit to associate with a diagnosis of cancer and genetic diseases. This functional method would lower a risk of such diseases by the early diagnosis. However, the high-intensity x-ray source, the highresolution x-ray detector, and more hair samples are necessarily desired to develop this x-ray technique and the efficiency would be enhanced by including the skin and fingernail samples with the human-hair analysis.

Keywords: Human-hair analysis, XRD, SAXS, breast cancer, health-state indicator

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Authors: M. Saravanan

Abstract:

Antimicrobial resistant is becoming a major factor in virtually all hospital acquired infection may soon untreatable is a serious public health problem. These concerns have led to major research effort to discover alternative strategies for the treatment of bacterial infection. Nanobiotehnology is an upcoming and fast developing field with potential application for human welfare. An important area of nanotechnology for development of reliable and environmental friendly process for synthesis of nanoscale particles through biological systems In the present studies are reported on the use of fungal strain Aspergillus species for the extracellular synthesis of bionanoparticles from 1 mM silver nitrate (AgNO3) solution. The report would be focused on the synthesis of metallic bionanoparticles of silver using a reduction of aqueous Ag+ ion with the culture supernatants of Microorganisms. The bio-reduction of the Ag+ ions in the solution would be monitored in the aqueous component and the spectrum of the solution would measure through UV-visible spectrophotometer The bionanoscale particles were further characterized by Atomic Force Microscopy (AFM), Fourier Transform Infrared Spectroscopy (FTIR) and Thin layer chromatography. The synthesized bionanoscale particle showed a maximum absorption at 385 nm in the visible region. Atomic Force Microscopy investigation of silver bionanoparticles identified that they ranged in the size of 250 nm - 680 nm; the work analyzed the antimicrobial efficacy of the silver bionanoparticles against various multi drug resistant clinical isolates. The present Study would be emphasizing on the applicability to synthesize the metallic nanostructures and to understand the biochemical and molecular mechanism of nanoparticles formation by the cell filtrate in order to achieve better control over size and polydispersity of the nanoparticles. This would help to develop nanomedicine against various multi drug resistant human pathogens.

Keywords: Bionanoparticles, UV-visible spectroscopy, AtomicForce Microscopy, Extracellular synthesis, Multi drug resistant, antimicrobial activity, Nanomedicine

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Authors: Samy A. Selim, Nashwa I. Hagag

Abstract:

Abstract–The objectives of the current study are to determine the prevalence, etiological agents, drug susceptibility pattern and plasmid profile of Acinetobacter baumannii isolates from Hospital-Acquired Infections (HAI) at Community Hospital, Al Jouf Province, Saudi Arabia. A total of 1890 patients had developed infection during hospital admission and were included in the study. Among those who developed nosocomial infections, 15(9.4), 10(2.7) and 118 (12.7) had respiratory tract infection (RTI), blood stream infections (BSI) and urinary tract (UTI) respectively. A total of 268 bacterial isolates were isolated from nosocomial infection. S. aureus was reported in 23.5% for of the total isolates followed by Klebsiella pneumoniae (17.5%), E. coli (17.2%), P. aeruginosa (11.9%), coagulase negative staphylococcus (9%), A. baumannii (7.1%), Enterobacter spp. (3.4%), Citrobacter freundii (3%), Proteus mirabilis (2.6%), and Proteus vulgaris and Enterococcous faecalis (0.7%). Isolated organisms are multi-drug resistant, predominantly Gram-positive pathogens with a high incidence of methicillin-resistant S. aureus, extended spectrum beta lactamase and vancomycin resistant enterococci organisms. The RFLP (Fragment Length Polymorphisms) patterns of plasmid preparations from isolated A. baumannii isolates had altered RFLP patterns, possibly due to the presence of plasmid(s). Five A. baumannii isolates harbored plasmids all of which were not less than 2.71kbp in molecular weight. Hence, it showed that the gene coding for the isolates were located on the plasmid DNA while the remaining isolates which have no plasmid might showed gene coding for antibiotic resistance being located on chromosomal DNA. Nosocomial infections represent a current problem in Community Hospital, Al Jouf Province, Saudi Arabia. Problems associated with SSI include infection with multidrug resistant pathogens which are difficult to treat and are associated with increased mortality.

Keywords: Hospital-Acquired Infections, Acinetobacter baumannii, antibiotic resistance, plasmid profile, RFLP patterns, Al Jouf Province, Saudi Arabia

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Authors: Paola Lecca, Lorenzo Dematte

Abstract:

Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.

Keywords: Reaction-diffusion systems, Fick's law, stochastic simulation algorithm.

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