Search results for: integral membrane protein folding

Authors: Abhay Asthana, Shally Toshkhani, Gyati Shilakari

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The present research was aimed to develop a biodegradable dermal patch formulation for wound healing in a novel, sustained and systematic manner. The goal is to reduce the frequency of dressings with improved drug delivery and thereby enhance therapeutic performance. In present study optimized formulation was designed using component polymers and excipients (e.g. Hydroxypropyl methyl cellulose, Ethylcellulose, and Gelatin) to impart significant folding endurance, elasticity and strength. Gelatin was used to get a mixture using ethylene glycol. Chitosan dissolved in suitable medium was mixed with stirring to gelatin mixture. With continued stirring to the mixture Curcumin was added in optimized ratio to get homogeneous dispersion. Polymers were dispersed with stirring in final formulation. The mixture was sonicated casted to get the film form. All steps were carried out under under strict aseptic conditions. The final formulation was a thin uniformly smooth textured film with dark brown-yellow color. The film was found to have folding endurance was around 20 to 21 times without a crack in an optimized formulation at RT (23C). The drug content was in range 96 to 102% and it passed the content uniform test. The final moisture content of the optimized formulation film was NMT 9.0%. The films passed stability study conducted at refrigerated conditions (4±0.2C) and at room temperature (23 ± 2C) for 30 days. Further, the drug content and texture remained undisturbed with stability study conducted at RT 23±2C for 45 and 90 days. Percentage cumulative drug release was found to be 80% in 12 h and matched the biodegradation rate as drug release with correlation factor R2 > 0.9. The film based formulation developed shows promising results in terms of stability and release profiles.

Keywords: biodegradable, patch, bioactive, polymer

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Authors: Elad Arad, Raz Jelinek, Hanna Rapaport

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Amyloidoses are a family of diseases characterized by abnormal protein folding that leads to aggregation. They accumulate to form fibrillar plaques which are implicated in the pathogenesis of Alzheimer, prion, diabetes type II and other diseases. To the best of our knowledge, despite extensive research efforts devoted to plaque aggregates inhibition, there is yet no cure for this phenomenon. Titanium and its alloys are found in growing interest for biomedical applications. Variety of surface modifications enable porous, adhesive, bioactive coatings for its surface. Titanium oxides (titania) are also being developed for photothermal and photodynamic treatments. Inspired by this, we set to explore the effect of functionalized titania nanoparticles in combination with external stimuli, as potential photothermal ablating agents against amyloids. Titania nanoparticles were coated with bi-functional catechol derivatives (dihydroxy-phenylalanine propanoic acid, noted DPA) to gain targeting properties. In conjunction with UV-radiation, these nanoparticles may selectively destroy the vicinity of their target. Titania modified 5 nm nanoparticles coated with DPA were further conjugated to the amyloid-targeting Congo Red (CR). These Titania-DPA-CR nanoparticles were found to target mature amyloid fibril of both amyloid-β (Aβ 1-42 a.a). Moreover, irradiation of the peptides in presence of the modified nanoparticles decreased the aggregate content and oligomer fraction. This work provides insights into the use of modified titania nanoparticles for amyloid plaque targeting and photothermal destruction. It may shed light on future modifications and functionalization of titania nanoparticles for different applications.

Keywords: titanium dioxide, amyloids, photothermal treatment, catechol, Congo-red

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Authors: Usha Kiran, M. Z. Abdin

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Osmotin is an abundant cationic multifunctional protein discovered in cells of tobacco (Nicotiana tabacum L. var Wisconsin 38) adapted to an environment of low osmotic potential. It provides plants protection from pathogens, hence placed in the PRP family of proteins. The osmotin induced proline accumulation has been reported in plants including transgenic tomato and strawberry conferring tolerance against both biotic and abiotic stresses. The exact mechanism of induction of proline by osmotin is however, not known till date. These observations have led us to hypothesize that osmotin induced proline accumulation could be due to its involvement as transcription factor and/or cell signal pathway modulator in proline biosynthesis. The present investigation was therefore, undertaken to analyze the osmotin protein as transcription factor /cell signalling modulator using bioinformatics tools. The results of available online DNA binding motif search programs revealed that osmotin does not contain DNA-binding motifs. The alignment results of osmotin protein with the protein sequence from DATF showed the homology in the range of 0-20%, suggesting that it might not contain a DNA binding motif. Further to find unique DNA-binding domain, the superimposition of osmotin 3D structure on modeled Arabidopsis transcription factors using Chimera also suggested absence of the same. We, however, found evidence implicating osmotin in cell signaling. With these results, we concluded that osmotin is not a transcription factor but regulating proline biosynthesis and accumulation through cell signaling during abiotic stresses.

Keywords: osmotin, cell signaling modulator, bioinformatic tools, protein

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Authors: Wen-Bao Qiao, Jean-Charles Créput

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To accelerate the solution for large scale traveling salesman problems (TSP), a parallel 2-opt local search algorithm with simple implementation based on Graphics Processing Unit (GPU) is presented and tested in this paper. The parallel scheme is based on technique of data decomposition by dynamically assigning multiple K processors on the integral tour to treat K edges’ 2-opt local optimization simultaneously on independent sub-tours, where K can be user-defined or have a function relationship with input size N. We implement this algorithm with doubly linked list on GPU. The implementation only requires O(N) memory. We compare this parallel 2-opt local optimization against sequential exhaustive 2-opt search along integral tour on TSP instances from TSPLIB with more than 10000 cities.

Keywords: parallel 2-opt, double links, large scale TSP, GPU

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Authors: F. Sabri, J. Jamali

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In this article, the wrinkling failure of orthotropic composite membranes due to in-plane shear deformation is investigated using nonlinear finite element analyses. A nonlinear post-buckling analysis is performed to show the evolution of shear-induced wrinkles. The method of investigation is based on the post-buckling finite element analysis adopted from commercial FEM code; ANSYS. The resulting wrinkling patterns, their amplitude and their wavelengths under the prescribed loads and boundary conditions were confirmed by experimental results. Our study reveals that wrinkles develop when both the magnitudes and coverage of the minimum principal stresses in the laminated composite laminates are sufficiently large to trigger wrinkling.

Keywords: composite, FEM, membrane, wrinkling

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Authors: Adesola Orimoloye, Edward Gobina

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Flue gas is the most prevalent source of carbon dioxide off-gas from numerous processes globally. Among the lion's share of this flue gas is the ever - present electric power plant, primarily fuelled by coal, and then secondly, natural gas. The carbon dioxide found in coal fired power plant off gas is among the dirtiest forms of carbon dioxide, even with many of the improvements in the plants; still this will yield sulphur and nitrogen compounds; among other rather nasty compounds and elements; all let to the atmosphere. This presentation will focus on the characterization of carbon dioxide-rich flue gas sources with a view of eventual conversion to chemicals and fuels using novel membrane reactors.

Keywords: Flue gas, carbon dioxide, membrane, catalyst, syngas

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Authors: Yehia Manawi, Ahmad Kayvanifard

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Membrane distillation is an emerging technology which has been used to produce freshwater and purify different types of aqueous mixtures. Qatar is an arid country where almost 100% of its freshwater demand is supplied through the energy-intensive thermal desalination process. The country’s need for water has reached an all-time high which stipulates finding an alternative way to augment freshwater without adding any drastic affect to the environment. The objective of this paper was to investigate the potential of using the industrial low grade waste heat to produce freshwater using membrane distillation. The main part of this work was conducting a heat audit on selected Qatari chemical industries to estimate the amounts of freshwater produced if such industrial waste heat were to be recovered. By the end of this work, the main objective was met and the heat audit conducted on the Qatari chemical industries enabled us to estimate both the amounts of waste heat which can be potentially recovered in addition to the amounts of freshwater which can be produced if such waste heat were to be recovered. By the end, the heat audit showed that around 605 Mega Watts of waste heat can be recovered from the studied Qatari chemical industries which resulted in a total daily production of 5078.7 cubic meter of freshwater. This water can be used in a wide variety of applications such as human consumption or industry. The amount of produced freshwater may look small when compared to that produced through thermal desalination plants; however, one must bear in mind that this water comes from waste and can be used to supply water for small cities or remote areas which are not connected to the water grid. The idea of producing freshwater from the two widely-available wastes (thermal rejected brine and waste heat) seems promising as less environmental and economic impacts will be associated with freshwater production which may in the near future augment the conventional way of producing freshwater currently being thermal desalination. This work has shown that low grade waste heat in the chemical industries in Qatar and perhaps the rest of the world can contribute to additional production of freshwater using membrane distillation without significantly adding to the environmental impact.

Keywords: membrane distillation, desalination, heat recovery, environment

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Authors: In-Hyuck Song, Jang-Hoon Ha

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Recently, porous ceramic membranes have attracted great interest due to their outstanding thermal and chemical stability. In this paper, we report the results of our efforts to determine whether we could prepare a diatomite-kaolin composite coating to be deposited over a sintered diatomite support layer that could reduce the largest pore size of the sintered diatomite membrane while retaining an acceptable level of permeability. We determined under what conditions such a composite coating over a support layer could be prepared without the generation of micro-cracks during drying and sintering. The pore characteristics of the sintered diatomite membranes were studied by scanning electron microscopy and capillary flow porosimetry.

Keywords: ceramic membrane, diatomite, water treatment, sintering

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Authors: Vassilis C. Moulianitis, Evgenios Scourboutis, Ilias Katsanis, Paraskevas Papanikos, Nikolas Zacharopoulos

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This paper presents the conceptual design of an automated biomethane potential measurement system. First, the design specifications for the BMP system and the basic components of the system will be presented. Three concepts that meet the design specifications will be presented. The basic characteristics of each concept will be analyzed in detail. The concepts will be evaluated using a set of design criteria that includes flexibility, cost, size, complexity, aesthetics, and accessibility in order to determine the best solution. The evaluation will be based on the discrete Choquet integral.

Keywords: automated biomethane test, conceptual mechatronics design, concept evaluation, Choquet integral

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Authors: Ripon Sarkar, Kabita Chaterjee, Ananya Barui

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Smoking is one of the leading causes of oral cancer. Cigarette smoke affects various cellular parameters and alters molecular metabolism of cells. Epithelial cells losses their cytoskeleton structure, membrane integrity, cellular polarity that subsequently initiates the process of epithelial cells to mesenchymal transition due to long exposure of cigarette smoking. It changes the normal cellular metabolic activity which induces oxidative stress and enhances the reactive oxygen spices (ROS) formation. Excessive ROS and associated oxidative stress are considered to be a driving force in alteration in cellular phenotypes, polarity distribution and mitochondrial metabolism. Noninvasive assessment of such parameters plays essential role in development of routine screening system for early diagnosis of oral cancer. Electrical cell-substrate impedance sensing (ECIS) is one of such method applied for detection of cellular membrane impedance which can be correlated to cell membrane integrity. Present study intends to explore the alteration in cellular impedance along with the expression of cellular polarity molecules and cytoskeleton distributions in oral epithelial cells of habitual smokers and to correlate the outcome to that of clinically diagnosed oral leukoplakia and oral squamous cell carcinoma patients. Total 80 subjects were categorized into four study groups: nonsmoker (NS), cigarette smoker (CS), oral leukoplakia (OLPK) and oral squamous cell carcinoma (OSCC). Cytoskeleton distribution was analyzed by staining of actin filament and generation of ROS was measured using assay kit using standard protocol. Cell impedance was measured through ECIS method at different frequencies. Expression of E-cadherin and protease-activated receptor (PAR) proteins were observed through immune-fluorescence method. Distribution of actin filament is well organized in NS group however; distribution pattern was grossly varied in CS, OLPK and OSCC. Generation of ROS was low in NS which subsequently increased towards OSCC. Expressions of E-cadherin and change in cellular electrical impedance in different study groups indicated the hallmark of cancer progression from NS to OSCC. Expressions of E-cadherin, PAR protein, and cell impedance were decreased from NS to CS and farther OSCC. Generally, the oral epithelial cells exhibit apico-basal polarity however with cancer progression these cells lose their characteristic polarity distribution. In this study expression of polarity molecule and ECIS observation indicates such altered pattern of polarity among smoker group. Overall the present study monitored the alterations in intracellular ROS generation and cell metabolic function, membrane integrity in oral epithelial cells in cigarette smokers. Present study thus has clinical significance, and it may help in developing a noninvasive technique for early diagnosis of oral cancer amongst susceptible individuals.

Keywords: cigarette smoking, early oral cancer detection, electric cell-substrate impedance sensing, noninvasive screening

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Authors: Manana Chumburidze

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We have considered a non-classical model of dynamical problems for a conjugated system of differential equations arising in thermo-piezoelectricity, which was formulated by Toupin – Mindlin. The basic concepts and the general theory of solvability for isotropic homogeneous elastic media is considered. They are worked by using the methods the Laplace integral transform, potential method and singular integral equations. Approximate solutions of mixed boundary value problems for finite domain, bounded by the some closed surface are constructed. They are solved in explicitly by using the generalized Fourier's series method.

Keywords: thermo-piezoelectricity, boundary value problems, Fourier's series, isotropic homogeneous elastic media

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Authors: Adesola O. Orimoloye, Edward Gobina

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Membrane separation technology is still considered as an emerging technology in the mining sector and does not yet have the widespread acceptance that it has in other industrial sectors. Underground Coal Gasification (UCG), wherein coal is converted to gas in-situ, is a safer alternative to mining method that retains all pollutants underground making the process environmentally friendly. In-situ combustion of coal for power generation allows access to more of the physical global coal resource than would be included in current economically recoverable reserve estimates. Where mining is no longer taking place, for economic or geological reasons, controlled gasification permits exploitation of the deposit (again a reaction of coal to form a synthesis gas) of coal seams in situ. The oxygen supply stage is one of the most expensive parts of any gasification project but the use of membranes is a potentially attractive approach for producing oxygen-enriched air. In this study, a variety of cost-effective membrane materials that gives an optimal amount of oxygen concentrations in the range of interest was designed and tested at diverse operating conditions. Oxygen-enriched atmosphere improves the combustion temperature but a decline is observed if oxygen concentration exceeds optimum. Experimental result also reveals the preparatory method, apparatus and performance of the fabricated membrane.

Keywords: membranes, oxygen-enrichment, gasification, coal

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Authors: Siyabonga Aubrey Mhlongo, Linda Lunga Sibali, Phumlane Selby Mdluli, Peter Papoh Ndibewu, Kholofelo Clifford Malematja

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This paper reports on the successful extraction and quantification of an antibacterial and antifungal agent present in some consumer products (Triclosan: C₁₂H₇Cl₃O₂)generally found in wastewater or effluents using molecularly imprinted membrane adsorbent (MIMs) followed by quantification and removal on a high-performance liquid chromatography (HPLC). Triclosan is an antibacterial and antifungal agent present in some consumer products like toothpaste, soaps, detergents, toys, and surgical cleaning treatments. The MIMs was fabricated usingpolyvinylidene fluoride (PVDF) polymer with selective micro composite particles known as molecularly imprinted polymers (MIPs)via a phase inversion by immersion precipitation technique. This resulted in an improved hydrophilicity and mechanical behaviour of the membranes. Wastewater samples were collected from the Umbogintwini Industrial Complex (UIC) (south coast of Durban, KwaZulu-Natal in South Africa). central UIC effluent treatment plant and pre-treated before analysis. Experimental parameters such as sample size, contact time, stirring speed were optimised. The resultant MIMs had an adsorption efficiency of 97% of TCS with reference to NIMs and bare membrane, which had 92%, 88%, respectively. The analytical method utilized in this review had limits of detection (LoD) and limits of quantification (LoQ) of 0.22, 0.71µgL-1 in wastewater effluent, respectively. The percentage recovery for the effluent samples was 68%. The detection of TCS was monitored for 10 consecutive days, where optimum TCS traces detected in the treated wastewater was 55.0μg/L inday 9 of the monitored days, while the lowest detected was 6.0μg/L. As the concentrations of analytefound in effluent water samples were not so diverse, this study suggested that MIMs could be the best potential adsorbent for the development and continuous progress in membrane technologyand environmental sciences, lending its capability to desalination.

Keywords: molecularly imprinted membrane, triclosan, phase inversion, wastewater

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Authors: Chijioke Okafor, Malik Maaza, Touhami Mokrani

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Proton exchange membrane, PEM was developed and tested for potential application in fuel cell. Nafion was electrospun to nanofiber network with the aid of poly(ethylene oxide), PEO, as a carrier polymer. The matrix polymer was crosslinked with Norland Optical Adhesive 63 under UV after compacting and annealing. The welded nanofiber mat was characterized for morphology, proton conductivity, and methanol permeability, then tested in a single cell test station. The results of the fabricated nanofiber membrane showed a proton conductivity of 0.1 S/cm at 25 oC and higher fiber volume fraction; methanol permeability of 3.6x10^-6 cm2/s and power density of 96.1 and 81.2 mW/cm2 for 5M and 1M methanol concentration respectively.

Keywords: fuel cell, nafion, nanofiber, permeability

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Authors: A. Rajabpour, A. Hadizadeh Kheirkhah

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Heat transfer is of great importance to biological systems in order to function properly. In the present study, specific heat capacity as one of the most important heat transfer properties is calculated for a soluble in water Lysozyme protein. Using equilibrium molecular dynamics (MD) simulation, specific heat capacities of pure water, dry lysozyme, and lysozyme-water solution are calculated at 300K for different weight fractions. It is found that MD results are in good agreement with ideal binary mixing rule at small weight fractions. Results of all simulations have been validated with experimental data.

Keywords: specific heat capacity, molecular dynamics simulation, lysozyme protein, equilibrium

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Authors: Jaeseung Lee, Muhammad Faizan Chinannai, Mohamed Hassan Gundu, Hyunchul Ju

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In this paper, we numerically investigated the effect of metal foams on a real scale 242.57cm2 (19.1 cm × 12.7 cm) polymer electrolyte membrane fuel cell (PEFCs) using a three-dimensional two-phase PEFC model to substantiate design approach for PEFCs using metal foam as the flow distributor. The simulations were conducted under the practical low humidity hydrogen, and air gases conditions in order to observe the detailed operation result in the PEFCs using the serpentine flow channel in the anode and metal foam design in the cathode. The three-dimensional contours of flow distribution in the channel, current density distribution in the membrane and hydrogen and oxygen concentration distribution are provided. The simulation results revealed that the use of highly porous and permeable metal foam can be beneficial to achieve a more uniform current density distribution and better hydration in the membrane under low inlet humidity conditions. This study offers basic directions to design channel for optimal water management of PEFCs.

Keywords: polymer electrolyte fuel cells, metal foam, real-scale, numerical model

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Authors: Taehoon Kwon, Hyeongrae Cho, Dirk Henkensmeier, Youngjong Kang, Chong Min Koo

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Ionic polymer actuators have been of interest in the bio-inspired artificial muscle devices. However, the relatively slow response and low power density were the obstacles for practical applications. In this study, ionic polymer actuators are fabricated with ionic polymer composite membranes based on sulfonated poly(arylene ether sulfone) (SPAES) and copper(II) phthalocyanine tetrasulfonic acid (CuPCSA). CuPCSA is an organic filler with very high ion exchange capacity (IEC, 4.5 mmol H+/g) that can be homogeneously dispersed on the molecular scale into the SPAES membrane. SPAES/CuPCSA actuators show larger ionic conductivity, mechanical properties, bending deformation, exceptional faster response to electrical stimuli, and larger mechanical power density (3028 W m–3) than Nafion actuators. This outstanding actuation performance of SPAES/CuPCSA composite membrane actuators makes them attractive for next generation transducers with high power density, which are currently developed biomimetic devices such as endoscopic surgery.

Keywords: actuation performance, composite membranes, ionic polymer actuators, organic filler

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Authors: Abdorrasoul Malekpour, Mohammad Ghorbani Mojtaba Mortazavi, Mohammadreza Fattahi, Mohammad Hassan Meshkibaf, Ali Fakhrzad, Saeid Salehi, Saeideh Zahedi, Amir Ahmadimoghaddam, Parviz Farzadnia Dr., Mohammadreza Hajyani Asl Bs

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Hepatitis B as an infectious disease has eight main genotypes (A–H). The aim of this study is to Bioinformatically identify Rare Codon Clusters (RCC) in proteins structure of HBV. For detection of protein family accession numbers (Pfam) of HBV proteins; used of uni-prot database and Pfam search tool were used. Obtained Pfam IDs were analyzed in Sherlocc program and RCCs in HBV proteins were detected. In further, the structures of TrEMBL entries proteins studied in PDB database and 3D structures of the HBV proteins and locations of RCCs were visualized and studied using Swiss PDB Viewer software. Pfam search tool have found nine significant hits and 0 insignificant hits in 3 frames. Results of Pfams studied in the Sherlocc program show this program not identified RCCs in the external core antigen (PF08290) and truncated HBeAg protein (PF08290). By contrast the RCCs become identified in Hepatitis core antigen (PF00906) Large envelope protein S (PF00695), X protein (PF00739), DNA polymerase (viral) N-terminal domain (PF00242) and Protein P (Pf00336). In HBV genome, seven RCC identified that found in hepatitis core antigen, large envelope protein S and DNA polymerase proteins and proteins structures of TrEMBL entries sequences that reported in Sherlocc program outputs are not complete. Based on situation of RCC in structure of HBV proteins, it suggested those RCCs are important in HBV life cycle. We hoped that this study provide a new and deep perspective in protein research and drug design for treatment of HBV.

Keywords: rare codon clusters, hepatitis B virus, bioinformatic study, infectious disease

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Authors: Dalia G. Aseel

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The potato (Solanum tubersum, L.) has become one of the major vegetable crops in Egypt and all over the world. Potato leafroll virus(PLRV) was observed on potato plants collected from different governorates in Egypt. Three cultivars, Spunta, Diamont, and Cara, infected with PLRV were collected; RNA was extracted and subjected to Real-Time PCR using the coat protein gene primers. The results showed that the expression of the coat protein was 39.6-fold, 12.45-fold, and 47.43-fold, respectively, for Spunta, Diamont, and Cara cultivars. Differential Display Polymerase Chain Reaction (DD-PCR) using pathogenesis-related protein 1 (PR-1), β-1,3-glucanases (PR-2), chitinase (PR-3), peroxidase (POD), and polyphenol oxidase (PPO) forward primers for pathogenesis-related proteins (PR). The obtained data revealed different banding patterns depending on the viral type and the region of infection. Regarding PLRV, 58 up-regulated and 19 down-regulated genes were detected. Sequence analysis of the up-and down-regulated genes revealed that infected plants were observed in comparison with the healthy control. Sequence analysis of the up-regulated gene was performed, and the encoding sequence analysis showed that the obtained genes include: induced stolen tip protein. On the other hand, two down-regulated genes were identified: disease resistance RPP-like protein and non-specific lipid-transfer protein. In this study, the expressions of PR-1, PR-2, PR-3, POD, and PPO genes in the infected leaves of three potato cultivars were estimated by quantitative real-time PCR. We can conclude that the PLRV-infection of potato plants inhibited the expression of the five PR genes. On the contrary, infected leaves by PLRV elevated the expression of some defense genes. This interaction may also induce and/or suppress the expression of some genes responsible for the plant's defense mechanisms.

Keywords: PLRV, pathogenesis-related proteins (PRs), DD-PCR, sequence, real-time PCR

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Authors: Farid Nouioua, Abdelouaheb Ardjouni

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In this article, we study the existence of positive periodic solutions of certain delay differential equations. In the process we convert the differential equation into an equivalent integral equation after which appropriate mappings are constructed. We then employ Krasnoselskii's fixed point theorem to obtain sufficient conditions for the existence of a positive periodic solution of the differential equation. The obtained results improve and extend the results in the literature. Finally, an example is given to illustrate our results.

Keywords: delay differential equations, positive periodic solutions, integral equations, Krasnoselskii fixed point theorem

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Authors: Angela U. Makolo

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Protein-coding and Non-coding regions determine the biology of a sequenced transcriptome. Research advances have shown that Non-coding regions are important in disease progression and clinical diagnosis. Existing bioinformatics tools have been targeted towards Protein-coding regions alone. Therefore, there are challenges associated with gaining biological insights from transcriptome sequence data. These tools are also limited to computationally intensive sequence alignment, which is inadequate and less accurate to identify both Protein-coding and Non-coding regions. Alignment-free techniques can overcome the limitation of identifying both regions. Therefore, this study was designed to develop an efficient sequence alignment-free model for identifying both Protein-coding and Non-coding regions in sequenced transcriptomes. Feature grouping and randomization procedures were applied to the input transcriptomes (37,503 data points). Successive iterations were carried out to compute the gradient vector that converged the developed Protein-coding and Non-coding Region Identifier (PNRI) model to the approximate coefficient vector. The logistic regression algorithm was used with a sigmoid activation function. A parameter vector was estimated for every sample in 37,503 data points in a bid to reduce the generalization error and cost. Maximum Likelihood Estimation (MLE) was used for parameter estimation by taking the log-likelihood of six features and combining them into a summation function. Dynamic thresholding was used to classify the Protein-coding and Non-coding regions, and the Receiver Operating Characteristic (ROC) curve was determined. The generalization performance of PNRI was determined in terms of F1 score, accuracy, sensitivity, and specificity. The average generalization performance of PNRI was determined using a benchmark of multi-species organisms. The generalization error for identifying Protein-coding and Non-coding regions decreased from 0.514 to 0.508 and to 0.378, respectively, after three iterations. The cost (difference between the predicted and the actual outcome) also decreased from 1.446 to 0.842 and to 0.718, respectively, for the first, second and third iterations. The iterations terminated at the 390th epoch, having an error of 0.036 and a cost of 0.316. The computed elements of the parameter vector that maximized the objective function were 0.043, 0.519, 0.715, 0.878, 1.157, and 2.575. The PNRI gave an ROC of 0.97, indicating an improved predictive ability. The PNRI identified both Protein-coding and Non-coding regions with an F1 score of 0.970, accuracy (0.969), sensitivity (0.966), and specificity of 0.973. Using 13 non-human multi-species model organisms, the average generalization performance of the traditional method was 74.4%, while that of the developed model was 85.2%, thereby making the developed model better in the identification of Protein-coding and Non-coding regions in transcriptomes. The developed Protein-coding and Non-coding region identifier model efficiently identified the Protein-coding and Non-coding transcriptomic regions. It could be used in genome annotation and in the analysis of transcriptomes.

Keywords: sequence alignment-free model, dynamic thresholding classification, input randomization, genome annotation

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Authors: You-Kai Jhang, Yang-Cheng Lu

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Major contributions of this study are threefold: designing a new model of planar-membrane humidifier for Proton Exchange Membrane Fuel Cell (PEMFC), an index to measure the Effectiveness (εT) of that humidifier, and an air compressor system to replicate related planar-membrane humidifier experiments. PEMFC as a kind of renewable energy has become more and more important in recent years due to its reliability and durability. To maintain the efficiency of the fuel cell, the membrane of PEMFC need to be controlled in a good hydration condition. How to maintain proper membrane humidity is one of the key issues to optimize PEMFC. We developed new humidifier to recycle water vapor from cathode air outlet so as to keep the moisture content of cathode air inlet in a PEMFC. By measuring parameters such as dry side air outlet dew point temperature, dry side air inlet temperature and humidity, wet side air inlet temperature and humidity, and differential pressure between dry side and wet side, we calculated indices obtained by dew point approach temperature (DPAT), water flux (J), water recovery ratio (WRR), effectiveness (εT), and differential pressure (ΔP). We discussed six topics including sealing effect, flow rate effect, flow direction effect, channel effect, temperature effect, and humidity effect by using these indices. Gas cylinders are used as sources of air supply in many studies of humidifiers. Gas cylinder depletes quickly during experiment at 1kW air flow rate, and it causes replication difficult. In order to ensure high stable air quality and better replication of experimental data, this study designs an air supply system to overcome this difficulty. The experimental result shows that the best rate of pressure loss of humidifier is 0.133×10³ Pa(g)/min at the torque of 25 (N.m). The best humidifier performance ranges from 30-40 (LPM) of air flow rates. The counter flow configured humidifies moisturizes the dry side inlet air more effectively than the parallel flow humidifier. From the performance measurements of the channel plates various rib widths studied in this study, it is found that the narrower the rib width is, the more the performance of humidifier improves. Raising channel width in same hydraulic diameter (Dh ) will obtain higher εT and lower ΔP. Moreover, increasing the dry side air inlet temperature or humidity will lead to lower εT. In addition, when the dry side air inlet temperature exceeds 50°C, the effect becomes even more obvious.

Keywords: PEM fuel cell, water management, membrane humidifier, heat and mass transfer, humidifier performance

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Authors: Marcin Stasiulewicz, Sebastian Filipkowski, Aneta Panuszko

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Background: The hallmark of neurodegenerative diseases, including Alzheimer's and Parkinson's diseases, is an aggregation of the abnormal forms of peptides and proteins. Water is essential to functioning biomolecules, and it is one of the key factors influencing protein folding and misfolding. However, the hydration studies of proteins are complicated due to the complexity of protein systems. The use of model compounds can facilitate the interpretation of results involving larger systems. Objectives: The goal of the research was to characterize the properties of the hydration water surrounding the two three-residue K peptide fragments INS (Isoleucine - Asparagine - Serine) and NSR (Asparagine - Serine - Arginine). Methods: Fourier-transform infrared spectra of aqueous solutions of the tripeptides were recorded on Nicolet 8700 spectrometer (Thermo Electron Co.) Measurements were carried out at 25°C for varying molality of solute. To remove oscillation couplings from water spectra and, consequently, obtain narrow O-D semi-heavy water bands (HDO), the isotopic dilution method of HDO in H₂O was used. The difference spectra method allowed us to isolate the tripeptide-affected HDO spectrum. Results: The structural and energetic properties of water affected by the tripeptides were compared to the properties of pure water. The shift of the values of the gravity center of bands (related to the mean energy of water hydrogen bonds) towards lower values with respect to the ones corresponding to pure water suggests that the energy of hydrogen bonds between water molecules surrounding tripeptides is higher than in pure water. A comparison of the values of the mean oxygen-oxygen distances in water affected by tripeptides and pure water indicates that water-water hydrogen bonds are shorter in the presence of these tripeptides. The analysis of differences in oxygen-oxygen distance distributions between the tripeptide-affected water and pure water indicates that around the tripeptides, the contribution of water molecules with the mean energy of hydrogen bonds decreases, and simultaneously the contribution of strong hydrogen bonds increases. Conclusions: It was found that hydrogen bonds between water molecules in the hydration sphere of tripeptides are shorter and stronger than in pure water. It means that in the presence of the tested tripeptides, the structure of water is strengthened compared to pure water. Moreover, it has been shown that in the vicinity of the Asparagine - Serine - Arginine, water forms stronger and shorter hydrogen bonds. Acknowledgments: This work was funded by the National Science Centre, Poland (grant 2017/26/D/NZ1/00497).

Keywords: amyloids, K-peptide, hydration, FTIR spectroscopy

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Authors: Maritza Granados Manjarrés

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This paper makes part of an investigation project which experiments with flat surfaces in order to pleat them using tessellations and flat origami conditions. The aim of the investigation is to eventually propose not only a methodology on how to pleat those surfaces but also to find an structural system to make them work as building skins. This stage of the investigation emphasizes on the experimentation with flat surfaces and different kinds of folding patterns and shows the many examples that can be made from this experimentation.

Keywords: flat origami, fold, space, surface

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Authors: Hameed Rukayat Opeyemi, Pericles Pilidis Pagone Emmanuele, Agbadede Roupa, Allison Isaiah

Abstract:

Climate change represents one of the single most challenging problems facing the world today. According to the National Oceanic and Administrative Association, Atmospheric temperature rose almost 25% since 1958, Artic sea ice has shrunk 40% since 1959 and global sea levels have risen more than 5.5cm since 1990. Power plants are the major culprits of GHG emission to the atmosphere. Several technologies have been proposed to reduce the amount of GHG emitted to the atmosphere from power plant, one of which is the less researched Advanced zero-emission power plant. The advanced zero emission power plants make use of mixed conductive membrane (MCM) reactor also known as oxygen transfer membrane (OTM) for oxygen transfer. The MCM employs membrane separation process. The membrane separation process was first introduced in 1899 when Walter Hermann Nernst investigated electric current between metals and solutions. He found that when a dense ceramic is heated, the current of oxygen molecules move through it. In the bid to curb the amount of GHG emitted to the atmosphere, the membrane separation process was applied to the field of power engineering in the low carbon cycle known as the Advanced zero emission power plant (AZEP cycle). The AZEP cycle was originally invented by Norsk Hydro, Norway and ABB Alstom power (now known as Demag Delaval Industrial turbomachinery AB), Sweden. The AZEP drew a lot of attention because its ability to capture ~100% CO2 and also boasts of about 30-50% cost reduction compared to other carbon abatement technologies, the penalty in efficiency is also not as much as its counterparts and crowns it with almost zero NOx emissions due to very low nitrogen concentrations in the working fluid. The advanced zero emission power plants differ from a conventional gas turbine in the sense that its combustor is substituted with the mixed conductive membrane (MCM-reactor). The MCM-reactor is made up of the combustor, low-temperature heat exchanger LTHX (referred to by some authors as air preheater the mixed conductive membrane responsible for oxygen transfer and the high-temperature heat exchanger and in some layouts, the bleed gas heat exchanger. Air is taken in by the compressor and compressed to a temperature of about 723 Kelvin and pressure of 2 Mega-Pascals. The membrane area needed for oxygen transfer is reduced by increasing the temperature of 90% of the air using the LTHX; the temperature is also increased to facilitate oxygen transfer through the membrane. The air stream enters the LTHX through the transition duct leading to inlet of the LTHX. The temperature of the air stream is then increased to about 1150 K depending on the design point specification of the plant and the efficiency of the heat exchanging system. The amount of oxygen transported through the membrane is directly proportional to the temperature of air going through the membrane. The AZEP cycle was developed using the Fortran software and economic analysis was conducted using excel and Matlab followed by optimization case study. The Simple bleed gas heat exchange layout (100 % CO2 capture), Bleed gas heat exchanger layout with flue gas turbine (100 % CO2 capture), Pre-expansion reheating layout (Sequential burning layout)–AZEP 85% (85% CO2 capture) and Pre-expansion reheating layout (Sequential burning layout) with flue gas turbine–AZEP 85% (85% CO2 capture). This paper discusses monte carlo risk analysis of four possible layouts of the AZEP cycle.

Keywords: gas turbine, global warming, green house gas, fossil fuel power plants

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Authors: Tety Hartatik, Dian Kurniawati, Adiarto

Abstract:

The aim of the research was to determine the associations between polymorphism of the bovine growth hormone (GH) gene (Leu/Val, L/V) and milk production of Friesian Holstein Cattle. A total of 62 cows which consist of two Friesian Holstein groups (cattle from New Zealand are 19 heads and cattle from Australia are 43 heads). We perform the PCR and RFLP method for analyzing the genotype of the target gene GH 211 bp in the part of intron 4 and exon 5 of GH gene. The frequencies of genotypes LL were higher than genotype LV. The number of genotype LL in New Zealand and Australia groups are 84% and 79%, respectively. The number of genotype LV in New Zealand and Australia groups are 16% and 21%, respectively. The association between Leu/Val polymorphism on milk production, fat and protein content in both groups does not show the significant effect. However base on the groups (cows from New Zealand compare with those from Australia) show the significant effect on fat and protein content.

Keywords: Friesian Holstein, fat content, growth hormone gene, milk production, PCR-RLFP, protein content

Procedia PDF Downloads 661

Authors: Leila Najafian

Abstract:

Sarcoplasmic protein hydrolysates (SPHs) and myofibrillar protein hydrolysates (MPHs) from patin (Pangasius sutchi) were produced using two types of proteases: Papain and Alcalase. 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) radical scavenging activities and metal chelating activity assays for antioxidant activities were carried out on the SPHs and MPHs. The hydrolysates were isolated and purified by ultrafiltration, gel filtration and reverse phase high-performance liquid chromatography (RP-HPLC) and liquid chromatography with tandem mass spectrometry detection (LC-MS/MS) was used in identifying peptide sequences. The results showed that when the DH of MPHs increased, the protein solubility increased, while the highest amount of the protein solubility of SPHs was after 60 min incubation. The effect of DH on antioxidant activities of SPHs and MPHs was investigated. Among the hydrolysates, papain-MPH and Alcalase-SPH, which had the highest antioxidant activities, were purified. The potent fractions obtained from RP-HPLC of sarcoplasmic (SI 3 fraction) and myofibrillar (MI 4 fraction) hydrolysates showed the highest DPPH radical scavenging activity. The FVNQPYLLYSVHMK peptide for MPH and the LVVDIPAALQHA peptide for SPH exhibited the highest antioxidant activity. The presence of hydrophobic and hydrophilic amino acids, namely leucine (L), valine (V), phenylalanine (F), histidine (H) and proline (P), in the peptide sequences of SPH and MPH are believed to contribute to high antioxidant activity. Hence, SPH and MPH from patin have the potential as a natural functional ingredient in food and pharmaceutical industry.

Keywords: patin (Pangasius sutchi), protein hydrolysates, antioxidative peptides, mass spectrometry

Procedia PDF Downloads 264

Authors: María José Bugueño, Natalia Jaime, Cristian Castro, Diego Naranjo, Guido Trautmann, Mario Pérez-Won, Vilbett Briones-Labarca

Abstract:

Proteins play a crucial role in various prepared foods, including dairy products, drinks, emulsions, and ready meals. These food proteins are naturally present in food waste and byproducts. The alkaline extraction and acid precipitation method is commonly used to extract proteins from plants and animals due to its product stability, cost-effectiveness, and ease of use. This study aimed to investigate the impact of pH-shifting storage at two different pH levels on the conformational changes affecting the physicochemical and functional properties of quinoa protein isolate (QPI) and yellow shrimp byproduct protein isolate (YSPI). The QPI and YSPI were extracted using the alkaline extraction-isoelectric precipitation method. The dispersions were adjusted to pH 4 or 12, stirred for 2 hours at 20°C to achieve a uniform dispersion, and then freeze-dried. Various analyses were conducted, including flexibility (F), free sulfhydryl content (Ho), emulsifying activity (EA), emulsifying capacity (EC), water holding capacity (WHC), oil holding capacity (OHC), intrinsic fluorescence, ultraviolet spectroscopy, differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR) to assess the properties of the protein isolates. pH-shifting at pH 11 and 12 for QPI and YSPI, respectively, significantly improved protein properties, while property modification of the samples treated under acidic conditions was less pronounced. Additionally, the pH 11 and 12 treatments significantly improved F, Ho, EA, WHC, OHC, intrinsic fluorescence, ultraviolet spectroscopy, DSC, and FTIR. The increase in Ho was due to disulfide bond disruption, which produced more protein sub-units than other treatments for both proteins. This study provides theoretical support for comprehensively elucidating the functional properties of protein isolates, promoting the application of plant proteins and marine byproducts. The pH-shifting process effectively improves the emulsifying property and stability of QPI and YSPI, which can be considered potential plant-based or marine byproduct-based emulsifiers for use in the food industry.

Keywords: quinoa protein, yellow shrimp by-product protein, physicochemical properties, structural properties

Procedia PDF Downloads 55

Authors: Hongping Lu, Kelbinur Tursun, Yaru Li, Yu Zhang, Shunai Liu, Ming Han

Abstract:

Objective: To investigate whether NS5ATP9 is involved in IL-6 mediated autophagy and the relationship between IL-6 and NS5ATP9 in liver cancer cells. Methods: 1. Detect the mRNA and protein levels of Beclin 1 after HepG2 cells were treated with or without recombinant human IL-6 protein. 2. Measure and compare of the changes of autophagy-related genes with their respective control, after IL-6 was silenced or neutralized with monoclonal antibody against human IL-6. 3. HepG2 cells were incubated with 50 ng/ml of IL-6 in the presence or absence of PDTC. The expression of NS5ATP9 was analyzed by Western blot after 48 h. 4. After NS5ATP9-silenced HepG2 cells had been treated with 50 ng/ml recombinant IL-6 protein, we detected the Beclin 1 and LC3B (LC3Ⅱ/Ⅰ) expression. 5. HepG2 cells were transfected with pNS5ATP9, si-NS5ATP9, and their respective control. Total RNA was isolated from cells and analyzed for IL-6. 6. Silence or neutralization of IL-6 in HepG2 cells which has been transfected with NS5ATP9. Beclin 1 and LC3 protein levels were analyzed by Western blot. Result: 1. After HepG2 were treated with recombinant human IL-6 protein, the expression of endogenous Beclin 1 was up-regulated at mRNA and protein level, and the conversion of endogenous LC3-I to LC3-II was also increased. These results indicated that IL-6 could induce autophagy. 2. When HepG2 cells were treated with IL-6 siRNA or monoclonal antibody against human IL-6, the expression of autophagy-related genes were decreased. 3. Exogenous human IL-6 recombinant protein up-regulated NS5ATP9 via NF-κB activation. 4. The expression of Beclin 1 and LC3B was down-regulated after IL-6 treated NS5ATP9-silenced HepG2 cells. 5. NS5ATP9 could reverse regulates IL-6 expression in HepG2 cells. 6. Silence or neutralization of IL-6 attenuates NS5ATP9-induced autophagy slightly. Conclusion: Our results implied that in HCC patients, maybe the higher level of IL-6 in the serum promoted the expression of NS5ATP9 and induced autophagy in cancer cells. And the over-expression of NS5ATP9 which induced by IL-6, in turn, increased IL-6 expression, further, promotes the IL-6/NS5ATP9-mediated autophagy and affects the progression of tumor. Therefore, NS5ATP9 silence might be a potential target for HCC therapy.

Keywords: autophagy, Hepatocellular carcinoma, IL-6, microenvironment, NS5ATP9

Procedia PDF Downloads 251

Authors: K. S. Zaytsev, Y. R. Nartsissov

Abstract:

Glycine is one of the key inhibitory neurotransmitters in Central nervous system (CNS) meanwhile glycinergic transmission is highly dependable on its appropriate reuptake from synaptic cleft. Glycine transporters (GlyT) of types 1 and 2 are the enzymes providing glycine transport back to neuronal and glial cells along with Na⁺ and Cl⁻ co-transport. The distribution and stoichiometry of GlyT1 and GlyT2 differ in details, and GlyT2 is more interesting for the research as it reuptakes glycine to neuron cells, whereas GlyT1 is located in glial cells. In the process of GlyT2 activity, the translocation of the amino acid is accompanied with binding of both one chloride and three sodium ions consequently (two sodium ions for GlyT1). In the present study, we developed a computer simulator of GlyT2 and GlyT1 activity based on known experimental data for quantitative estimation of membrane glycine transport. The trait of a single protein functioning was described using the probability approach where each enzyme state was considered separately. Created scheme of transporter functioning realized as a consequence of elemental steps allowed to take into account each event of substrate association and dissociation. Computer experiments using up-to-date kinetic parameters allowed receiving the number of translocated glycine molecules, Na⁺ and Cl⁻ ions per time period. Flexibility of developed software makes it possible to evaluate glycine reuptake pattern in time under different internal characteristics of enzyme conformational transitions. We investigated the behavior of the system in a wide range of equilibrium constant (from 0.2 to 100), which is not determined experimentally. The significant influence of equilibrium constant in the range from 0.2 to 10 on the glycine transfer process is shown. The environmental conditions such as ion and glycine concentrations are decisive if the values of the constant are outside the specified range.

Keywords: glycine, inhibitory neurotransmitters, probability approach, single protein functioning

Procedia PDF Downloads 123