Search results for: protein structure

Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

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Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast.

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Authors: Bahareh Hajirostamloo

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Cow milk, is a product of the mammary gland and soymilk is a beverage made from soybeans; it is the liquid that remains after soybeans are soaked. In this research effort, we compared nutritional parameters of this two kind milk such as total fat, fiber, protein, minerals (Ca, Fe and P), fatty acids, carbohydrate, lactose, water, total solids, ash, pH, acidity and calories content in one cup (245 g). Results showed soymilk contains 4.67 grams of fat, 0.52 of fatty acids, 3.18 of fiber, 6.73 of protein, 4.43 of carbohydrate, 0.00 of lactose, 228.51 of water, 10.40 of total solids and 0.66 of ash, also 9.80 milligrams of Ca, 1.42 of Fe, and 120.05 of P, 79 Kcal of calories, pH=6.74 and acidity was 0.24%. Cow milk contains 8.15 grams of fat, 5.07 of fatty acids, 0.00 of fiber, 8.02 of protein, 11.37 of carbohydrate, ´Çá4.27 of lactose, 214.69 of water, 12.90 of total solids, 1.75 of ash, 290.36 milligrams of Ca, 0.12 of Fe, and 226.92 of P, 150 Kcal of calories, pH=6.90 and acidity was 0.21% . Soy milk is one of plant-based complete proteins and cow milk is a rich source of nutrients as well. Cow milk is containing near twice as much fat as and ten times more fatty acids do soymilk. Cow milk contains greater amounts of mineral (except Fe) it contain more than three hundred times the amount of Ca and nearly twice the amount of P as does soymilk but soymilk contains more Fe (ten time more) than does cow milk. Cow milk and soy milk contain nearly identical amounts of protein and water and fiber is a big plus, dairy has none. Although what we choose to drink is really a mater of personal preference and our health objectives but looking at the comparison, soy looks like healthier choices.

Keywords: Soymilk, cow milk, nutritional, comparison.

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Authors: Xu Zhang, Qi Jiang, Liwei Li, Weiwei Cui, Jijun Cui, Yang Cao, Hairong Zhao

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A kind of crash energy absorption structure adopted by vehicle simulator crash testing equipment based on mechanical energy storage was studied. Dynamic explicit finite element simulation was achieved for thin-walled tube structure under different conditions of section shape, thickness and inducement groove style. Crash energy absorption property of the structure was obtained. After optimization, a reasonable structure was given which can meet current vehicle crash regulation. And the optimized structure can be adopted in vehicle simulator, which can increase the practicability of the testing equipment.

Keywords: thin-walled tube structure, crash energy absorption, deceleration, finite element simulation

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Authors: Océane Grosset, Charles Pézerat, Jean-Hugh Thomas, Frédéric Ablitzer

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This paper presents a method to take into account the fluid-structure coupling into an inverse method, the Force Analysis Technique (FAT). The FAT method, also called RIFF method (Filtered Windowed Inverse Resolution), allows to identify the force distribution from local vibration field. In order to only identify the external force applied on a structure, it is necessary to quantify the fluid-structure coupling, especially in naval application, where the fluid is heavy. This method can be decomposed in two parts, the first one consists in identifying the fluid-structure coupling and the second one to introduced it in the FAT method to reconstruct the external force. Results of simulations on a plate coupled with a cavity filled with water are presented.

Keywords: Fluid-structure coupling, inverse methods, naval, vibrations.

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

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

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

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Authors: Noha A. Mohammed, Isam A. Mohamed Ahmed, Elfadil E. Babiker

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The present study was carried out to evaluate the nutritional value of sorghum flour during processing of injera (unleavened thick bread). The proximate composition of sorghum flour before and after fermentation and that of injera was determined. Compared to the raw flour and fermented one, injera had low protein (11.55%), ash (1.57%) and fat (2.40%) contents but high in fiber content. Moreover, injera was found to have significantly (P ≤ 0.05) higher energy (389.08 Kcal/100g) compared to raw and fermented sorghum flour. Injera contained lower levels of anti-nutritional factors (polyphenols, phytate and tannins) compared to raw and fermented sorghum. Also it was found to be rich in Ca (4.75mg/100g), Fe (3.95 mg/100g), and Cu (0.7 mg/100g) compared to that of raw and fermented flour. Moreover, both the extractable minerals and protein digestibility were high for injera due to low amount of anti-nutrients. Injera was found to contain an appreciable amount of amino acids except arginine and tyrosine.

Keywords: Cooking, Fermentation, Malt, Protein fractions, Sorghum.

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Authors: Rosarin Rujananon, Poonsuk Prasertsan, Amornrat Phongdara, Tanate Panrat, Jibin Sun, Sugima Rappert, An-Ping Zeng

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In this study, a synthetic pathway was created by assembling genes from Clostridium butyricum and Escherichia coli in different combinations. Among the genes were dhaB1 and dhaB2 from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt) and its activator (GDHtAc), respectively, involved in the conversion of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene from E.coli BL21 was also included which codes for an NADPHdependent 1,3-propanediol oxidoreductase isoenzyme (PDORI) reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling analysis indicated that the conformation of fusion protein of YQHD and DHAB1 was favorable for direct molecular channeling of the intermediate 3-HPA. According to the simulation results, the yqhD and dhaB1 gene were assembled in the upstream of dhaB2 to express a fusion protein, yielding the recombinant strain E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing the recombinant enzymes simultaneously but in a non-fusion mode. This is the first report using a gene fusion approach to enhance the biological conversion of glycerol to the value added compound 1,3- PD.

Keywords: Recombinant E.coli, 1, 3-propanediol, glycerol, fusion protein.

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Authors: Arun Kumar V.A., Keshav Mohan

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Adenylate kinase (AK) catalyse the phosphotransferase reaction plays an important role in cellular energy homeostasis. The inhibitors of bacterial AK are useful in the treatment of several bacterial infections. To the novel inhibitors of AK, docking studies performed by using the 3D structure of Bacillus stearothermophilus adenylate kinase from protein data bank (IZIP). 46 Quinoxaline analogues were docked in 1ZIP and selected the highly interacting compounds based on their binding energies, for further studies

Keywords: Kinase, quinoxaline, homeostasis, inhibitor, nucleotide.

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Authors: Yanhua Jin, Won Suk Lee

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The two-dimensional gel electrophoresis method (2-DE) is widely used in Proteomics to separate thousands of proteins in a sample. By comparing the protein expression levels of proteins in a normal sample with those in a diseased one, it is possible to identify a meaningful set of marker proteins for the targeted disease. The major shortcomings of this approach involve inherent noises and irregular geometric distortions of spots observed in 2-DE images. Various experimental conditions can be the major causes of these problems. In the protein analysis of samples, these problems eventually lead to incorrect conclusions. In order to minimize the influence of these problems, this paper proposes a partition based pair extension method that performs spot-matching on a set of gel images multiple times and segregates more reliable mapping results which can improve the accuracy of gel image analysis. The improved accuracy of the proposed method is analyzed through various experiments on real 2-DE images of human liver tissues.

Keywords: Proteomics, spot-matching, two-dimensionalelectrophoresis.

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Authors: Rizkita R. Esyanti, Iriawati, Olga Mardisadora

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Vetiver oil is secondary metabolite that accumulates in Vetiveria zizanioides roots.  The aim of this study was to obtain best type of root culture which produce high amount of vetiver oil, and was similar to metabolites produce from its mother plant.  Protein analysis was also conducted to detect protein, related to putative enzymes, which have a role in terpenoids synthesis in the root culture. The results showed that root culture derived from crown explant produced the best root growth.   The root culture produced primary and lateral roots, ca. 40 branches.  The vetiver oil produced from root culture was analyzed by using GC-MS., and the highest content of terpenoids from roots of crown explant attained 19.024%.  The result of SDS PAGE showed proteins which were ±61 kD and ± 68 kD, each might be related to putative monoterpene synthase and sesquiterpenes complex, respectively. 

Keywords: Protein, Root culture, Terpenoids, Vetiver oil.

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Authors: P. Tej, P. Kněž, M. Blank

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The paper presents design and production of thin-walled U-profile footbridge made of UHPFRC. The main structure of the bridge is one prefabricated shell structure made of UHPFRC with dispersed steel fibers without any conventional reinforcement. The span of the bridge structure is 10 m and the clear width of 1.5 m. The thickness of the UHPFRC shell structure oscillated in an interval of 30-45 mm. Several calculations were made during the bridge design and compared with the experiments. For the purpose of verifying the calculations, a segment of 1.5 m was first produced, followed by the whole footbridge for testing. After the load tests were done, the design was optimized to cast the final footbridge.

Keywords: Footbridge, UHPFRC, non-linear analysis, shell structure.

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Authors: Oh Hyeon Jeon, WooYoung Jung

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In this study, seepage analysis was performed by the level difference between upstream and downstream of weir structure for safety evaluation of weir structure against flooding. Monte Carlo Simulation method was employed by considering the probability distribution of the adjacent ground parameter, i.e., permeability coefficient of weir structure. Moreover, by using a commercially available finite element program (ABAQUS), modeling of the weir structure is carried out. Based on this model, the characteristic of water seepage during flooding was determined at each water level with consideration of the uncertainty of their corresponding permeability coefficient. Subsequently, fragility function could be constructed based on this response from numerical analysis; this fragility function results could be used to determine the weakness of weir structure subjected to flooding disaster. They can also be used as a reference data that can comprehensively predict the probability of failur,e and the degree of damage of a weir structure.

Keywords: Weir structure, seepage, flood disaster fragility, probabilistic risk assessment, Monte-Carlo Simulation, permeability coefficient.

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Authors: Payel Ghosh, Rama Chandra Pradhan, Sabyasachi Mishra

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Jamun (Syzygium cuminii L.) is one of the important indigenous minor fruit with high medicinal value. The jamun cultivation is unorganized and there is huge loss of this fruit every year. The perishable nature of the fruit makes its postharvest management further difficult. Due to the strong cell wall structure of pectin-protein bonds and hard seeds, extraction of juice becomes difficult. Enzymatic treatment has been commercially used for improvement of juice quality with high yield. The objective of the study was to optimize the best treatment method for juice extraction. Enzymes (Pectinase and Tannase) from different stains had been used and for each enzyme, best result obtained by using response surface methodology. Optimization had been done on the basis of physicochemical property, nutritional property, sensory quality and cost estimation. According to quality aspect, cost analysis and sensory evaluation, the optimizing enzymatic treatment was obtained by Pectinase from Aspergillus aculeatus strain. The optimum condition for the treatment was 44 ^oC with 80 minute with a concentration of 0.05% (w/w). At these conditions, 75% of yield with turbidity of 32.21NTU, clarity of 74.39%T, polyphenol content of 115.31 mg GAE/g, protein content of 102.43 mg/g have been obtained with a significant difference in overall acceptability.

Keywords: Jamun, enzymatic treatment, physicochemical property, sensory analysis, optimization.

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Authors: Lili Chen, Chao Yuan

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On path space kQ, there is a trivial kQ^a-module structure determined by the multiplication of path algebra kQ^a and a trivial kQ^c-comodule structure determined by the comultiplication of path coalgebra kQ^c. In this paper, on path space kQ, a nontrivial kQ^a-module structure is defined, and it is proved that this nontrivial left kQ^a-module structure is isomorphic to the dual module structure of trivial right kQ^c-comodule. Dually, on path space kQ, a nontrivial kQ^c-comodule structure is defined, and it is proved that this nontrivial right kQ^c-comodule structure is isomorphic to the dual comodule structure of trivial left kQ^a-module. Finally, the trivial and nontrivial module structures on path space are compared from the aspect of submodule, and the trivial and nontrivial comodule structures on path space are compared from the aspect of subcomodule.

Keywords: Quiver, path space, module, comodule, dual.

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Authors: Chia-Ta Tsai, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Shinn-Ying Ho

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Prediction of bacterial virulent protein sequences can give assistance to identification and characterization of novel virulence-associated factors and discover drug/vaccine targets against proteins indispensable to pathogenicity. Gene Ontology (GO) annotation which describes functions of genes and gene products as a controlled vocabulary of terms has been shown effectively for a variety of tasks such as gene expression study, GO annotation prediction, protein subcellular localization, etc. In this study, we propose a sequence-based method Virulent-GO by mining informative GO terms as features for predicting bacterial virulent proteins. Each protein in the datasets used by the existing method VirulentPred is annotated by using BLAST to obtain its homologies with known accession numbers for retrieving GO terms. After investigating various popular classifiers using the same five-fold cross-validation scheme, Virulent-GO using the single kind of GO term features with an accuracy of 82.5% is slightly better than VirulentPred with 81.8% using five kinds of sequence-based features. For the evaluation of independent test, Virulent-GO also yields better results (82.0%) than VirulentPred (80.7%). When evaluating single kind of feature with SVM, the GO term feature performs much well, compared with each of the five kinds of features.

Keywords: Bacterial virulence factors, GO terms, prediction, protein sequence.

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Authors: Natalya G. Filimonova, Mariya G. Ozerova, Irina N. Ermakova

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The long-term strategy of the economic development of Russia up to 2030 is based on the concept of sustainable growth. The determining factor of such development is complex changes in the economic system which may be achieved by making progressive changes in its structure. The structural changes determine the character and the direction of economic development, as well as they include all elements of this system without exception, and their regulated character ensures the most rapid aim achievement. This article has discussed the industrial structure of the agriculture in Russia. With the use of the system of indexes, the article has determined the directions, intensity, and speed of structural shifts. The influence of structural changes on agricultural production development has been found out. It is noticed that the changes in the industrial structure are synchronized with the changes in the organisation and economic structure. Efficiency assessment of structural changes allowed to trace the efficiency of structural changes and elaborate the main directions for agricultural policy improvement.

Keywords: Russian agriculture system, sectoral structure, organizational and economic structure, structural changes.

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Authors: Erhan Ata, Yusuf Yaylı

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Let M be an almost split quaternionic manifold on which its almost split quaternionic structure is defined by a three dimensional subbundle V of ( T M) T (M) * Ôèù and {F,G,H} be a local basis for V . Suppose that the (global) (1, 2) tensor field defined[V ,V ]is defined by [V,V ] = [F,F]+[G,G] + [H,H], where [,] denotes the Nijenhuis bracket. In ref. [7], for the almost split-hypercomplex structureH = J α,α =1,2,3, and the Obata connection ÔêçH vanishes if and only if H is split-hypercomplex. In this study, we give a prof, in particular, prove that if either M is a split quaternionic Kaehler manifold, or if M is a splitcomplex manifold with almost split-complex structure F , then the vanishing [V ,V ] is equivalent to that of all the Nijenhuis brackets of {F,G,H}. It follows that the bundle V is trivial if and only if [V ,V ] = 0 .

Keywords: Almost split - hypercomplex structure, Almost split quaternionic structure, Almost split quaternion Kaehler manifold, Obata connection.

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Authors: Fan-Yong Meng

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In this paper, a generalized form of the Banzhaf-Owen value for cooperative fuzzy games with a coalition structure is proposed. Its axiomatic system is given by extending crisp case. In order to better understand the Banzhaf-Owen value for fuzzy games with a coalition structure, we briefly introduce the Banzhaf-Owen values for two special kinds of fuzzy games with a coalition structure, and give their explicit forms.

Keywords: Cooperative fuzzy game, Banzhaf-Owen value, multi linear extension, Choquet integral.

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Authors: Hanina M. N., Hairul Shahril M., Mohd Fazrullah Innsan M. F., Ismatul Nurul Asyikin I., Abdul Jalil A. K, Salina M. R., Ahmad I.B.

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Proteins levels produced by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antimicrobial agents or antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics or natural compounds in nature as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was focusing on the effect of essential oils from Cymbopogon flexuosus and C. nardus in regulating proteins production by Bacillus subtilis ATCC 21332. The Minimum Inhibition Concentrations (MICs) of both essential oils on B. subtilis were determined by using microdilution assay, resulting 0.2% and 1.56% for each C. flexuosus and C. nardus subsequently. The bacteria were further exposed to each essential oils at concentration of 0.01XMIC for 2 days. The proteins were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Protein profile showed that a band with approximate size of 250 kD was appeared for the treated bacteria with essential oils. Thus, Bacillus subtilis ATCC 21332 in stressful condition with the presence of essential oils at low concentration could induce the protein production.

Keywords: Bacillus subtilis ATCC 21332, Cymbopogon essential oils, protein

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Authors: Uun Yanuhar

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The purpose of research was to know the role of immunogenic protein of 49 kDa from V.alginolyticus which capable to initiate molecule expression of MHC Class II in receptor of Cromileptes altivelis. The method used was in vivo experimental research through testing of immunogenic protein 49 kDa from V.alginolyticus at Cromileptes altivelis (size of 250 - 300 grams) using 3 times booster by injecting an immunogenic protein in a intramuscular manner. Response of expressed MHC molecule was shown using immunocytochemistry method and SEM. Results indicated that adhesin V.alginolyticus 49 kDa which have immunogenic character could trigger expression of MHC class II on receptor of grouper and has been proven by staining using immunocytochemistry and SEM with labeling using antibody anti MHC (anti mouse). This visible expression based on binding between epitopes antigen and antibody anti MHC in the receptor. Using immunocytochemistry, intracellular response of MHC to in vivo induction of immunogenic adhesin from V.alginolyticus was shown.

Keywords: C.altivelis, immunogenic, MHC, V.alginolyticus.

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Authors: Sirilak Namwong , Wonnop Visessanguan, Soottawat Benjakul, Somboon Tanasupawat

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The halophilic proteinase showed a maximal activity at 50°C and pH 9~10, in 20% NaCl and was highly stabilized by NaCl. It was able to hydrolyse natural actomyosin (NAM), collagen and anchovy protein. For NAM hydrolysis, the myosin heavy chain was completely digested by halophilic proteinase as evidenced by the lowest band intensity remaining, but partially hydrolysed actin. The SR5-3 proteinase was also capable hydrolyzing two major components of collagen, β- and α-compounds, effectively. The degree of hydrolysis (DH) of the halophilic proteinase and commercial proteinases (Novozyme, Neutrase, chymotrypsin and Flavourzyme) on the anchovy protein, were compared, and it was found that the proteinase showed a greater degree of hydrolysis towards anchovy protein than that from commercial proteinases. DH of halophilic proteinase was sharply enhanced according to the increase in the concentration of enzyme from 0.035 U to 0.105 U. The results warranting that the acceleration of the production of fish sauce with higher quality, may be achieved by adding of the halophilic proteinase from this bacterium.

Keywords: Halophilic proteinase, Halobacillus sp. SR5-3, anchovy (Spolephorus spp.) proteins, fish sauce

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Authors: Samira Laidaoui, Mohammed Djermane, Nazihe Terfaya

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The fluid-structure coupling is a natural phenomenon which reflects the effects of two continuums: fluid and structure of different types in the reciprocal action on each other, involving knowledge of elasticity and fluid mechanics. The solution for such problems is based on the relations of continuum mechanics and is mostly solved with numerical methods. It is a computational challenge to solve such problems because of the complex geometries, intricate physics of fluids, and complicated fluid-structure interactions. The way in which the interaction between fluid and solid is described gives the largest opportunity for reducing the computational effort. In this paper, a problem of fluid structure interaction is investigated with two-way coupling method. The formulation Arbitrary Lagrangian-Eulerian (ALE) was used, by considering a dynamic grid, where the solid is described by a Lagrangian formulation and the fluid by a Eulerian formulation. The simulation was made on the ANSYS software.

Keywords: ALE, coupling, FEM, fluid-structure interaction, one-way method, two-way method.

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: Begomovirus, AV1 gene, sequence, cloning, whitefly, okra, cotton, tomato, RAPD, phylogenetic tree and SDS-PAGE.

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Authors: R. K. Singh, P. K. Jain

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In the present paper, disc loaded interaction structure for potential application in wideband Gyro-TWT amplifier has been analyzed, taking all the space and modal harmonics into consideration, for the eigenwave solutions. The analysis has been restricted to azimuthally symmetric TE0,n mode. Dispersion characteristics have been plotted by varying the structure parameters and have been validated against HFSS simulation results. The variation of eigenvalue with respect to different structure parameters has also been presented. It has been observed that disc periodicity plays very important role for wideband operation of disc-loaded Gyro-TWT.

Keywords: Broadbanding, Disc-loaded interaction structure, Eigenvalue, Gyro-TWT, HFSS.

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Authors: M. R. Jokanović, V. M. Tomović, M. T. Jović, S. B. Škaljac, B. V. Šojić, P. M. Ikonić, T. A. Tasić

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Proximate (moisture, protein, total fat, total ash) and mineral (K, P, Na, Mg, Ca, Zn, Fe, Cu and Mn) composition of chicken giblets (heart, liver and gizzard) were investigated. Phosphorous content, as well as proximate composition, were determined according to recommended ISO methods. The content of all elements, except phosphorus, of the giblets tissues were determined using inductively coupled plasma-optical emission spectrometry (ICP-OES), after dry ashing mineralization. Regarding proximate composition heart was the highest in total fat content, and the lowest in protein content. Liver was the highest in protein and total ash content, while gizzard was the highest in moisture and the lowest in total fat content. Regarding mineral composition liver was the highest for K, P, Ca, Mg, Fe, Zn, Cu, and Mn, while heart was the highest for Na content. The contents of almost all investigated minerals in analysed giblets tissues of chickens from Vojvodina were similar to values reported in the literature, i.e. in national food composition databases of other countries.

Keywords: Chicken giblets, proximate composition, mineral composition.

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Authors: N. Hussain, G. Jaffery, A.N. Sabri, S. Hasnain

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The main aim is to perform mutational analysis of CTLA4 gene Exon 1 in SLE patients. A total of 61 SLE patients fulfilling “American College of Rheumatology (ACR) criteria" and 61 controls were enrolled in this study. The region of CTLA4 gene exon 1 was amplified by using Step-down PCR technique. Extracted DNA of band 354 bp was sequenced to analyze mutations in the exon-1 of CTLA-4 gene. Further, protein sequences were identified from nucleotide sequences of CTLA4 Exon 1 by using Expasy software and through Blast P software it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. No variations were found after patients sequences were compared with that of the control sequence. Furthermore it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. Thus CTLA4 gene may not be responsible for an autoimmune disease SLE.

Keywords: American College of Rheumatology criteria, autoimmune disease, Cytotoxic T Lymphocyte Antigen-4, Polymerase Chain Reaction, Systemic Lupus Erythematosus

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Authors: Mahmoud Miri, Soleiman Maramaee

Abstract:

Because of architectural condition and structure application, sometimes mass source and stiffness source are not coincidence, and the structure is irregular. The structure is also might be asymmetric as an asymmetric bracing in plan which leads to unbalance distribution of stiffness or because of unbalance distribution of the mass. Both condition lead to eccentricity and torsion in the structure. The deficiency of ordinary code to evaluate the performance of steel structures against earthquake has been caused designing based on performance level or capacity spectrum be used. By using the mentioned methods it is possible to design a structure that its behavior against different earthquakes be predictive. In this article 5- story buildings with different percentage of asymmetric which is because of stiffness changes have been designed. The static and dynamic nonlinear analysis under three acceleration recording has been done. Finally performance level of the structure has been evaluated.

Keywords: Seismic analysis, torsion, asymmetric, irregular building, stiffness source.

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Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

Abstract:

The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: Nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation.

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

Abstract:

Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

Abstract:

Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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