Search results for: protein interaction network
10239 Functional Properties of Sunflower Protein Concentrates Extracted Using Different Anti-greening Agents - Low-Fat Whipping Cream Preparation
Authors: Tamer M. El-Messery
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By-products from sunflower oil extraction, such as sunflower cakes, are rich sources of proteins with desirable functional properties for the food industry. However, challenges such as sensory drawbacks and the presence of phenolic compounds have hindered their widespread use. In this study, sunflower protein concentrates were obtained from sunflower cakes using different ant-greening solvents (ascorbic acid (ASC) and N-acetylcysteine (NAC)), and their functional properties were evaluated. The color of extracted proteins ranged from dark green to yellow, where the using of ASC and NAC agents enhanced the color. The protein concentrates exhibited high solubility (>70%) and antioxidant activity, with hydrophobicity influencing emulsifying activity. Emulsions prepared with these proteins showed stability and microencapsulation efficiency. Incorporation of protein concentrates into low-fat whipping cream formulations increased overrun and affected color characteristics. Rheological studies demonstrated pseudoplastic behavior in whipped cream, influenced by shear rates and protein content. Overall, sunflower protein isolates showed promising functional properties, indicating their potential as valuable ingredients in food formulations.Keywords: functional properties, sunflower protein concentrates, antioxidant capacity, ant-greening agents, low-fat whipping cream
Procedia PDF Downloads 3410238 Tail-Binding Effect of Kinesin-1 Auto Inhibition Using Elastic Network Model
Authors: Hyun Joon Chang, Jae In Kim, Sungsoo Na
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Kinesin-1 (hereafter called kinesin) is a molecular motor protein that moves cargos toward the end of microtubules using the energy of adenosine triphosphate (ATP) hydrolysis. When kinesin is inactive, its tail autoinhibits the motor chain in order to prevent from reacting with the ATP by cross-linking of the tail domain to the motor domains at two positions. However, the morphological study of kinesin during autoinhibition is yet remained obscured. In this study, we report the effect of the binding site of the tail domain using the normal mode analysis of the elastic network model on kinesin in the tail-free form and tail-bind form. Considering the relationship between the connectivity of conventional network model with respect to the cutoff length and the functionality of the binding site of the tail, we revaluated the network model to observe the key role of the tail domain in its structural aspect. Contingent on the existence of the tail domain, the results suggest the morphological stability of the motor domain. Furthermore, employing the results from normal mode analysis, we have determined the strain energy of the neck linker, an essential portion of the motor domain for ATP hydrolysis. The results of the neck linker also converge to the same indication, i.e. the morphological analysis of the motor domain.Keywords: elastic network model, Kinesin-1, autoinhibition
Procedia PDF Downloads 44710237 MICA-TM Peptide Selectively Binds to HLAs Associated with Behçet's Disease
Authors: Sirilak Kongkaew, Pathumwadee Yodmanee, Nopporn Kaiyawet, Arthitaya Meeprasert, Thanyada Rungrotmongkol, Toshikatsu Kaburaki, Hiroshi Noguchi, Fujio Takeuch, Nawee Kungwan, Supot Hannongbua
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Behçet’s disease (BD) is a genetic autoimmune expressed by multisystemic inflammatory disorder mostly occurred at the skin, joints, gastrointestinal tract, and genitalia, including ocular, oral, genital, and central nervous systems. Most BD patients in Japan and Korea were strongly indicated by the genetic factor namely HLA-B*51 (especially, HLA-B*51:01) marker in HMC class I, while HLA-A*26:01 allele has been detected from the BD patients in Greek, Japan, and Taiwan. To understand the selective binding of the MICA-TM peptide towards the HLAs associated with BD, the molecular dynamics simulations were applied on the four HLA alleles (B*51:01, B*35:01, A*26:01, and A*11:01) in complex with such peptide. As a result, the key residues in the binding groove of HLA protein which play an important role in the MICA-TM peptide binding and stabilization were revealed. The Van der Waals force was found to be the main protein-protein interaction. Based on the binding free energy prediction by MM/PBSA method, the MICA-TM peptide interacted stronger to the HLA alleles associated to BD in the identical class by 7-12 kcal/mol. The obtained results from the present study could help to differentiate the HLA alleles and explain a source of Behçet’s disease.Keywords: Behçet’s disease, MD simulations, HMC class I, autoimmune
Procedia PDF Downloads 39110236 Effect of Extrusion Processing Parameters on Protein in Banana Flour Extrudates: Characterisation Using Fourier-Transform Infrared Spectroscopy
Authors: Surabhi Pandey, Pavuluri Srinivasa Rao
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Extrusion processing is a high-temperature short time (HTST) treatment which can improve protein quality and digestibility together with retaining active nutrients. In-vitro protein digestibility of plant protein-based foods is generally enhanced by extrusion. The current study aimed to investigate the effect of extrusion cooking on in-vitro protein digestibility (IVPD) and conformational modification of protein in green banana flour extrudates. Green banana flour was extruded through a co-rotating twin-screw extruder varying the moisture content, barrel temperature, screw speed in the range of 10-20 %, 60-80 °C, 200-300 rpm, respectively, at constant feed rate. Response surface methodology was used to optimise the result for IVPD. Fourier-transform infrared spectroscopy (FTIR) analysis provided a convenient and powerful means to monitor interactions and changes in functional and conformational properties of extrudates. Results showed that protein digestibility was highest in extrudate produced at 80°C, 250 rpm and 15% feed moisture. FTIR analysis was done for the optimised sample having highest IVPD. FTIR analysis showed that there were no changes in primary structure of protein while the secondary protein structure changed. In order to explain this behaviour, infrared spectroscopy analysis was carried out, mainly in the amide I and II regions. Moreover, curve fitting analysis showed the conformational changes produced in the flour due to protein denaturation. The quantitative analysis of the changes in the amide I and II regions provided information about the modifications produced in banana flour extrudates.Keywords: extrusion, FTIR, protein conformation, raw banana flour, SDS-PAGE method
Procedia PDF Downloads 15210235 Protein-Thiocyanate Composite as a Sensor for Iron III Cations
Authors: Hosam El-Sayed, Amira Abou El-Kheir, Salwa Mowafi, Marwa Abou Taleb
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Two proteinic biopolymers; namely keratin and sericin, were extracted from their respective natural resources by simple appropriate methods. The said proteins were dissolved in the appropriate solvents followed by regeneration in a form of film polyvinyl alcohol. Proteinium thiocyanate (PTC) composite was prepared by reaction of a regenerated film with potassium thiocyanate in acid medium. In another experiment, the said acidified proteins were reacted with potassium thiocyante before dissolution and regeneration in a form of PTC composite. The possibility of using PTC composite for determination of the concentration of iron III ions in domestic as well as industrial water was examined. The concentration of iron III cations in water was determined spectrophotometrically by measuring the intensity of blood red colour of iron III thiocyanate obtained by interaction of PTC with iron III cation in the tested water sample.Keywords: iron III cations, protein, sensor, thiocyanate, water
Procedia PDF Downloads 42210234 Regulation of PKA-Dependent Calcineurin as a Switch in Cell Secretion
Authors: Hani M. M. Alothaid, Louise Robson, Richmond Muimo
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This study will investigate cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) dependent calcineurin (Cn), known as protein phosphatase 2 B (PP2B) as well, regulation of chloride ion (Cl⁻) secretion and the release of pro-inflammatory molecules in immune cells such as cytokines. THP-1-derived monocytes, primary human monocytes and the bronchial epithelial cell line (16HBE14o-) were used in this study. The 16HBE14o- cells were chosen as positive control. Hence, to further confirm the expression of cystic fibrosis transmembrane conductance regulator (CFTR), calcium binding protein (S100A10), annexin A2 (AnxA2) and calcineurin A subunit (CnA) in all three cell types, cell lysate was probed against corresponding primary antibodies by immunoblotting. Western blot analyses show the expression of CFTR, AnxA2, CnA and S100A10 in THP-1-derived monocytes and primary human monocytes. In conclusion, CFTR, S100A10, CnA and AnxA2 are expressed in THP-1-derived monocytes and primary human monocytes and regulate Cl⁻ secretion. Also, they may play a role in the pro-inflammatory molecules release. The ongoing work will confirm interaction between these proteins in the cell lines.Keywords: annexin A2, calcineurin, CFTR, chloride, monocytes, pro-inflammatory molecules, S100A10
Procedia PDF Downloads 22910233 Value Added by Spirulina Platensis in Two Different Diets on Growth Performance, Gut Microbiota, and Meat Quality of Japanese Quails
Authors: Mohamed Yusuf
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Aim: The growth promoting the effect of the blue-green filamentous alga Spirulina platensis (SP) was observed on meat type Japanese quail with antibiotic growth promoter alternative and immune enhancing power. Materials and Methods: This study was conducted on 180 Japanese quail chicks for 4 weeks to find out the effect of diet type (vegetarian protein diet [VPD] and fish meal protein diet [FMPD])- Spirulina dose interaction (1 or 2 g/kg diet) on growth performance, gut microbiota, and sensory meat quality of growing Japanese quails (1-5 weeks old). Results: Data revealed improvement (p<0.05) of weight gain, feed conversion ratio, and European efficiency index due to 1, 2 g (SP)/kg VPD, and 2 g (SP)/kg FMPD, respectively. There was a significant decrease of ileum mean pH value by 1 g(SP)/kg VPD. Concerning gut microbiota, there was a trend toward an increase in Lactobacilli count in both 1; 2 g (SP)/kgVPD and 2 g (SP)/kg FMPD. It was concluded that 1 or 2 g (SP)/kg vegetarian diet may enhance parameters of performance without obvious effect on both meat quality and gut microbiota. Moreover, 1 and/or 2 g (SP) may not be invited to share fishmeal based diet for growing Japanese quails. Conclusion: Using of SP will support the profitable production of Japanese quails fed vegetable protein diet.Keywords: isocaloric, isonitrogenous, meat quality, performances, quails, spirulina, spirulina
Procedia PDF Downloads 24610232 Mechanism of Modeling the Level of Bcr-Abl Oncoprotein by Ubiquitin-Proteasome System in Chronic Myeloid Leukemia
Authors: Svitlana Antonenko, Gennady Telegeev
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Introductive statement: The development of chronic myeloid leukemia (CML) is caused by Bcr-Abl oncoprotein. Modern treatments with tyrosine kinase inhibitors are greatly complicated by the mutational variability of the Bcr-Abl oncoprotein, which causes drug resistance. Therefore, there is an urgent need to develop new approaches to the treatment of the disease, which will allow modeling the level of Bcr-Abl oncoprotein in the cell. Promising in this direction is the identification of proteases that can selectively promote cellular proteolysis of oncoproteins. The aim of the study was to study the effect of the interaction of Bcr-Abl with deubiquitinase USP1 on the level of oncoprotein in CML cells. Methodology: K562 cells were selected for the experiment. Сells were incubated with ML323 inhibitor for 24 hours. Precipitation of endogenous proteins from K562 cell lysate was performed using anti-Bcr-Abl antibodies. Cell lysates and precipitation results were studied by Western blot. Subcellular localization of proteins was studied by immunofluorescence analysis followed by confocal microscopy. The results were analyzed quantitatively and statistically. Major findings: The Bcr-Abl/USP1 protein complex was detected in CML cells, and it was found that inhibition of USP1 deubiquitinating activity by the compound ML323 leads to disruption of this protein complex and a decrease in the level of Bcr-Abl oncoprotein in cells. The interaction of Bcr-Abl with USP1 may result in deubiquitination of the oncoprotein, which disrupts its proteasomal degradation and leads to the accumulation of CML in cells. Conclusion: We believe that the interaction of oncoprotein with USP1 may be one of the prerequisites that contribute to malignant cell transformation due to the deubiquitination of oncoprotein, which leads to its accumulation and disease progression. A correlation was found between the deubiquitinating activity of USP1 and the level of oncoprotein in CML cells. Thus, we identify deubiquitinase USP1 as a promising therapeutic target for the development of a new strategy for the treatment of CML by modulating the level of Bcr-Abl in the cell.Keywords: chronic myeloid leukemia, Bcr-Abl, USP1, deubiquitination Bcr-Abl, K562 cell
Procedia PDF Downloads 6310231 Physicochemical Properties of Pea Protein Isolate (PPI)-Starch and Soy Protein Isolate (SPI)-Starch Nanocomplexes Treated by Ultrasound at Different pH Values
Authors: Gulcin Yildiz, Hao Feng
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Soybean proteins are the most widely used and researched proteins in the food industry. Due to soy allergies among consumers, however, alternative legume proteins having similar functional properties have been studied in recent years. These alternative proteins are also expected to have a price advantage over soy proteins. One such protein that has shown good potential for food applications is pea protein. Besides the favorable functional properties of pea protein, it also contains fewer anti-nutritional substances than soy protein. However, a comparison of the physicochemical properties of pea protein isolate (PPI)-starch nanocomplexes and soy protein isolate (SPI)-starch nanocomplexes treated by ultrasound has not been well documented. This study was undertaken to investigate the effects of ultrasound treatment on the physicochemical properties of PPI-starch and SPI-starch nanocomplexes. Pea protein isolate (85% pea protein) provided by Roquette (Geneva, IL, USA) and soy protein isolate (SPI, Pro-Fam® 955) obtained from the Archer Daniels Midland Company were adjusted to different pH levels (2-12) and treated with 5 minutes of ultrasonication (100% amplitude) to form complexes with starch. The soluble protein content was determined by the Bradford method using BSA as the standard. The turbidity of the samples was measured using a spectrophotometer (Lambda 1050 UV/VIS/NIR Spectrometer, PerkinElmer, Waltham, MA, USA). The volume-weighted mean diameters (D4, 3) of the soluble proteins were determined by dynamic light scattering (DLS). The emulsifying properties of the proteins were evaluated by the emulsion stability index (ESI) and emulsion activity index (EAI). Both the soy and pea protein isolates showed a U-shaped solubility curve as a function of pH, with a high solubility above the isoelectric point and a low one below it. Increasing the pH from 2 to 12 resulted in increased solubility for both the SPI and PPI-starch complexes. The pea nanocomplexes showed greater solubility than the soy ones. The SPI-starch nanocomplexes showed better emulsifying properties determined by the emulsion stability index (ESI) and emulsion activity index (EAI) due to SPI’s high solubility and high protein content. The PPI had similar or better emulsifying properties at certain pH values than the SPI. The ultrasound treatment significantly decreased the particle sizes of both kinds of nanocomplex. For all pH levels with both proteins, the droplet sizes were found to be lower than 300 nm. The present study clearly demonstrated that applying ultrasonication under different pH conditions significantly improved the solubility and emulsify¬ing properties of the SPI and PPI. The PPI exhibited better solubility and emulsifying properties than the SPI at certain pH levelsKeywords: emulsifying properties, pea protein isolate, soy protein isolate, ultrasonication
Procedia PDF Downloads 30910230 Chitosan-Whey Protein Isolate Core-Shell Nanoparticles as Delivery Systems
Authors: Zahra Yadollahi, Marjan Motiei, Natalia Kazantseva, Petr Saha
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Chitosan (CS)-whey protein isolate (WPI) core-shell nanoparticles were synthesized through self-assembly of whey protein isolated polyanions and chitosan polycations in the presence of tripolyphosphate (TPP) as a crosslinker. The formation of this type of nanostructures with narrow particle size distribution is crucial for developing delivery systems since the functional characteristics highly depend on their sizes. To achieve this goal, the nanostructure was optimized by varying the concentrations of WPI, CS, and TPP in the reaction mixture. The chemical characteristics, surface morphology, and particle size of the nanoparticles were evaluated.Keywords: whey protein isolated, chitosan, nanoparticles, delivery system
Procedia PDF Downloads 8510229 Survivable IP over WDM Network Design Based on 1 ⊕ 1 Network Coding
Authors: Nihed Bahria El Asghar, Imen Jouili, Mounir Frikha
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Inter-datacenter transport network is very bandwidth and delay demanding. The data transferred over such a network is also highly QoS-exigent mostly because a huge volume of data should be transported transparently with regard to the application user. To avoid the data transfer failure, a backup path should be reserved. No re-routing delay should be observed. A dedicated 1+1 protection is however not applicable in inter-datacenter transport network because of the huge spare capacity. In this context, we propose a survivable virtual network with minimal backup based on network coding (1 ⊕ 1) and solve it using a modified Dijkstra-based heuristic.Keywords: network coding, dedicated protection, spare capacity, inter-datacenters transport network
Procedia PDF Downloads 43910228 Aptamers: A Potential Strategy for COVID-19 Treatment
Authors: Mohamad Ammar Ayass, Natalya Griko, Victor Pashkov, Wanying Cao, Kevin Zhu, Jin Zhang, Lina Abi Mosleh
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Respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Early evidence pointed at the angiotensin-converting enzyme 2 (ACE-2) expressed on the epithelial cells of the lung as the main entry point of SARS-CoV-2 into the cells. The viral entry is mediated by the binding of the Receptor Binding Domain (RBD) of the spike protein that is expressed on the surface of the virus to the ACE-2 receptor. As the number of SARS-CoV-2 variants continues to increase, mutations arising in the RBD of SARS-CoV-2 may lead to the ineffectiveness of RBD targeted neutralizing antibodies. To address this limitation, the objective of this study is to develop a combination of aptamers that target different regions of the RBD, preventing the binding of the spike protein to ACE-2 receptor and subsequent viral entry and replication. A safe and innovative biomedical tool was developed to inhibit viral infection and reduce the harms of COVID-19. In the present study, DNA aptamers were developed against a recombinant trimer S protein using the Systematic Evolution of Ligands by Exponential enrichment (SELEX). Negative selection was introduced at round number 7 to select for aptamers that bind specifically to the RBD domain. A series of 9 aptamers (ADI2010, ADI2011, ADI201L, ADI203L, ADI205L, ADIR68, ADIR74, ADIR80, ADIR83) were selected and characterized with high binding affinity and specificity to the RBD of the spike protein. Aptamers (ADI25, ADI2009, ADI203L) were able to bind and pull down endogenous spike protein expressed on the surface of SARS-CoV-2 virus in COVID-19 positive patient samples and determined by liquid chromatography- tandem mass spectrometry analysis (LC-MS/MS). LC-MS/MS data confirmed that aptamers can bind to the RBD of the spike protein. Furthermore, results indicated that the combination of the 9 best aptamers inhibited the binding of the purified trimer spike protein to the ACE-2 receptor found on the surface of Vero E6 cells. In the same experiment, the combined aptamers displayed a better neutralizing effect than antibodies. The data suggests that the selected aptamers could be used in therapy to neutralize the effect of the SARS-CoV-2 virus by inhibiting the interaction between the RBD and ACE-2 receptor, preventing viral entry into target cells and therefore blocking viral replication.Keywords: aptamer, ACE-2 receptor, binding inhibitor, COVID-19, spike protein, SARS-CoV-2, treatment
Procedia PDF Downloads 18010227 Novel Recommender Systems Using Hybrid CF and Social Network Information
Authors: Kyoung-Jae Kim
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Collaborative Filtering (CF) is a popular technique for the personalization in the E-commerce domain to reduce information overload. In general, CF provides recommending items list based on other similar users’ preferences from the user-item matrix and predicts the focal user’s preference for particular items by using them. Many recommender systems in real-world use CF techniques because it’s excellent accuracy and robustness. However, it has some limitations including sparsity problems and complex dimensionality in a user-item matrix. In addition, traditional CF does not consider the emotional interaction between users. In this study, we propose recommender systems using social network and singular value decomposition (SVD) to alleviate some limitations. The purpose of this study is to reduce the dimensionality of data set using SVD and to improve the performance of CF by using emotional information from social network data of the focal user. In this study, we test the usability of hybrid CF, SVD and social network information model using the real-world data. The experimental results show that the proposed model outperforms conventional CF models.Keywords: recommender systems, collaborative filtering, social network information, singular value decomposition
Procedia PDF Downloads 28210226 The Application on Interactivity of Light in New Media Art
Authors: Yansong Chen
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In the age of media convergence, new media technology is constantly impacting, changing, and even reshaping the limits of Art. From the technological ontology of the new media art, the concept of interaction design has always been dominated by I/O (Input/Output) systems through the ages, which ignores the content of systems and kills the aura of art. Light, as a fusion media, basically comes from the extension of some human feelings and can be the content of the input or the effect of output. In this paper, firstly, on the basis of literature review, the interaction characteristics research was conducted on light. Secondly, starting from discourse patterns of people and machines, people and people, people, and imagining things, we propose three light modes: object-oriented interaction, Immersion interaction, Tele-Presence interaction. Finally, this paper explains how to regain the aura of art through light elements in new media art and understand multiple levels of 'Interaction design'. In addition, the new media art, especially the light-based interaction art, enriches the language patterns and motivates emerging art forms to be more widespread and popular, which achieves its aesthetics growth.Keywords: new media art, interaction design, light art, immersion
Procedia PDF Downloads 22910225 Effects of High-Protein, Low-Energy Diet on Body Composition in Overweight and Obese Adults: A Clinical Trial
Authors: Makan Cheraghpour, Seyed Ahmad Hosseini, Damoon Ashtary-Larky, Saeed Shirali, Matin Ghanavati, Meysam Alipour
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Background: In addition to reducing body weight, the low-calorie diets can reduce the lean body mass. It is hypothesized that in addition to reducing the body weight, the low-calorie diets can maintain the lean body mass. So, the current study aimed at evaluating the effects of high-protein diet with calorie restriction on body composition in overweight and obese individuals. Methods: 36 obese and overweight subjects were divided randomly into two groups. The first group received a normal-protein, low-energy diet (RDA), and the second group received a high-protein, low-energy diet (2×RDA). The anthropometric indices including height, weight, body mass index, body fat mass, fat free mass, and body fat percentage were evaluated before and after the study. Results: A significant reduction was observed in anthropometric indices in both groups (high-protein, low-energy diets and normal-protein, low-energy diets). In addition, more reduction in fat free mass was observed in the normal-protein, low-energy diet group compared to the high -protein, low-energy diet group. In other the anthropometric indices, significant differences were not observed between the two groups. Conclusion: Independently of the type of diet, low-calorie diet can improve the anthropometric indices, but during a weight loss, high-protein diet can help the fat free mass to be maintained.Keywords: diet, high-protein, body mass index, body fat percentage
Procedia PDF Downloads 30010224 Force Measurement for E-Cadherin-Mediated Intercellular Adhesion Probed by Protein Micropattern and Traction Force Microscopy
Authors: Chieh-Chung Tsou, Chun-Min Lo, Yeh-Shiu Chu
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Cell’s mechanical forces provide important physical cues in regulation of proper cellular functions, such as cell differentiation, proliferation and migration. It is believed that adhesive forces generated by cell-cell interaction are able to transmit to the interior of cell through filamentous cortical cytoskeleton. Prominent among other membrane receptors, Cadherins are prototypical adhesive molecules able to generate remarkable forces to regulate intercellular adhesion. However, the mechanistic steps of mechano-transduction in Cadherin-mediated adhesion remain very controversial. We are interested in understanding how Cadherin protein complexes enable force generation and transmission at cell-cell contact in the initial stage of intercellular adhesion. For providing a better control of time, space, and substrate stiffness, in this study, a combination of protein micropattern, micropipette manipulation, and traction force microscopy is used. Pair micropattern with different forms confines cell spreading area and the gaps in pairs varied from 2 to 8 microns are applied for monitoring the forces that cell pairs generated, measured by traction force microscopy. Moreover, cell clones obtained from epithelial cells undergone genome editing are used to score the importance for known components of Cadherin complexes in force generation. We believe that our results from this combinatory mechanobiological method will provide deep insights on understanding the biophysical principle governing mechano- transduction of Cadherin-mediated intercellular adhesion.Keywords: cadherin, intercellular adhesion, protein micropattern, traction force microscopy
Procedia PDF Downloads 24810223 Region-Specific Secretory Protein, α2M, in Male Reproductive Tract of the Blue Crab And Its Dynamics during Sperm transit towards Female Spermatheca
Authors: Thanyaporn Senarai, Rapeepun Vanichviriyakit, Shinji Miyata, Chihiro Sato, Prapee Sretarugsa, Wattana Weerachatyanukul, Ken Kitajima
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In this study, we characterized a region-specific 250 kDa protein that was secreted of MSD fluid, which is believed to play dual functions in forming a spermatophoric wall for sperm physical protection, and in sperm membrane modification as part of sperm maturation process. The partial amino acid sequence and N-terminal sequencing revealed that the MSD-specific 250 kDa protein showed a high similarity with a plasma-rich protein, α-2 macroglobulin (α2M), so termed pp-α2M. This protein was a large glycoprotein contained predominantly mannose and GlcNAc. The expression of pp-α2M mRNA was detected in spermatic duct (SD), androgenic gland (AG) and hematopoietic tissue, while the protein expression was rather specific to the apical cytoplasm of MSD epithelium. The secretory pp-α2M in MSD fluid was acquired onto the MSD sperm membrane and was also found within the matrix of the acrosome. Distally, pp-α2M was removed from spermathecal sperm membrane, while its level kept constant in the sperm AC. Together the results indicate that pp-α2M is a 250 kDa region-specific secretory protein which plays roles in sperm physical protection and also acts as maturation factor in the P. pelagicus sperm.Keywords: alpha-2 macroglobulin, blue swimming crab, sperm maturation, spermatic duct
Procedia PDF Downloads 32310222 Easymodel: Web-based Bioinformatics Software for Protein Modeling Based on Modeller
Authors: Alireza Dantism
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Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller
Procedia PDF Downloads 8810221 Self-Reliance Support and Environment Interaction in Long-Term Care
Authors: Chen-Yuan Hsu
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Introduction Elderly is growing and results to live in the long-term care (LTC) and then due to the routine of the facilities in Taiwan, also resulted to losing of those people with environment interaction, so, the self-reliance support (SRS) for those people to experience environment interaction is an essential. Methods This study was recruited samples of a LTC in the central of Taiwan. There was a following research on the SRS group with 20 samples collected and routine care group with 20 samples. A structured questionnaire as the Environment Interaction Dimension, as data collection included demographic information and the dimensions of environment interaction. Data analysis used SPSS 22.0 for Window 2000 to report the finding. Results The Environment Interaction Dimension for Taiwanese is a Chinese version of the containing 8 items. The result of t-test analysis found that environment interaction showed a significant difference between groups (p<.05), the result recommended that there was a higher score of environment interaction dimension on the SRS group (29.90±5.56) comparing with the routine care group (22.1±5.53). Conclusion This study showed that the SRS group was higher than the routine care group on the environment interaction dimension for Taiwanese elderly living in the LTC. The results can also provide the reference for LTC, to encourage those people to participate in SRS in LTC, and therefore also improving their environment interaction.Keywords: self-reliance support, environment interaction, long-term care, elderly
Procedia PDF Downloads 9510220 Bioinformatics Approach to Identify Physicochemical and Structural Properties Associated with Successful Cell-free Protein Synthesis
Authors: Alexander A. Tokmakov
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Cell-free protein synthesis is widely used to synthesize recombinant proteins. It allows genome-scale expression of various polypeptides under strictly controlled uniform conditions. However, only a minor fraction of all proteins can be successfully expressed in the systems of protein synthesis that are currently used. The factors determining expression success are poorly understood. At present, the vast volume of data is accumulated in cell-free expression databases. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with successful cell-free expression. Here, we describe an approach aimed at identification of multiple physicochemical and structural properties of amino acid sequences associated with protein solubility and aggregation and highlight major correlations obtained using this approach. The developed method includes: categorical assessment of the protein expression data, calculation and prediction of multiple properties of expressed amino acid sequences, correlation of the individual properties with the expression scores, and evaluation of statistical significance of the observed correlations. Using this approach, we revealed a number of statistically significant correlations between calculated and predicted features of protein sequences and their amenability to cell-free expression. It was found that some of the features, such as protein pI, hydrophobicity, presence of signal sequences, etc., are mostly related to protein solubility, whereas the others, such as protein length, number of disulfide bonds, content of secondary structure, etc., affect mainly the expression propensity. We also demonstrated that amenability of polypeptide sequences to cell-free expression correlates with the presence of multiple sites of post-translational modifications. The correlations revealed in this study provide a plethora of important insights into protein folding and rationalization of protein production. The developed bioinformatics approach can be of practical use for predicting expression success and optimizing cell-free protein synthesis.Keywords: bioinformatics analysis, cell-free protein synthesis, expression success, optimization, recombinant proteins
Procedia PDF Downloads 41310219 Study of Eatable Aquatic Invertebrates in the River Dhansiri, Dimapur, Nagaland, India
Authors: Dilip Nath
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A study has been conducted on the available aquatic invertebrates in the river Dhansiri at Dimapur site. The study confirmed that the river body composed of aquatic macroinvertebrate community under two phyla viz., Arthropods and Molluscs. Total 10 species have been identified from there as the source of alternative protein food for the common people. Not only the protein source, they are also the component of aquatic food chain and indicators of aquatic ecosystem. Proper management and strategies to promote the edible invertebrates can be considered as the alternative protein and alternative income source for the common people for sustainable livelihood improvement.Keywords: Dhansiri, Dimapur, invertebrates, livelihood improvement, protein
Procedia PDF Downloads 14410218 Protein and MDA (Malondialdehyde) Profil of Bull Sperm and Seminal Plasma After Freezing
Authors: Sri Rahayu, M. Dwi Susan, Aris Soewondo, W. M. Agung Pramana
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Semen is an organic fluid (seminal plasma) that contain spermatozoa. Proteins are one of the major seminal plasma components that modulate sperm functionality, influence sperm capacitation and maintaining the stability of the membrane. Semen freezing is a procedure to preserve sperm cells. The process causes decrease in sperm viability due to temperature shock and oxidation stress. Oxidation stress is a disturbance on phosphorylation that increases ROS concentration, and it produces lipid peroxide in spermatozoa membrane resulted in high MDA (malondialdehyde) concentration. The objective of this study was to examine the effect of freezing on protein and MDA profile of bovine sperm cell and seminal plasma after freezing. Protein and MDA of sperm cell and seminal plasma were isolated from 10 sample. Protein profiles was analyzed by SDS PAGE with separating gel 12,5 %. The concentration of MDA was measured by spectrophotometer. The results of the research indicated that freezing of semen cause lost of the seminal plasma proteins with molecular with 20, 10, and 9 kDa. In addition, the result research showed that protein of the sperm (26, 10, 9, 7, and 6 kDa) had been lost. There were difference MDA concentration of seminal plasma and sperm cell were increase after freezing. MDA concentration of seminal plasma before and after freezing were 2.2 and 2.4 nmol, respectively. MDA concentration of sperm cell before and after freezing were 1,5 and 1.8 nmol, respectively. In conclusion, there were differences protein profiles of spermatozoa before and after semen freezing and freezing cause increasing of the MDA concentration.Keywords: MDA, semen freezing, SDS PAGE, protein profile
Procedia PDF Downloads 26910217 Study on Energy Performance Comparison of Information Centric Network Based on Difference of Network Architecture
Authors: Takumi Shindo, Koji Okamura
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The first generation of the wide area network was circuit centric network. How the optimal circuit can be signed was the most important issue to get the best performance. This architecture had succeeded for line based telephone system. The second generation was host centric network and Internet based on this architecture has very succeeded world widely. And Internet became as new social infrastructure. Currently the architecture of the network is based on the location of the information. This future network is called Information centric network (ICN). The information-centric network (ICN) has being researched by many projects and different architectures for implementation of ICN have been proposed. The goal of this study is to compare performances of those ICN architectures. In this paper, the authors propose general ICN model which can represent two typical ICN architectures and compare communication performances using request routing. Finally, simulation results are shown. Also, we assume that this network architecture should be adapt to energy on-demand routing.Keywords: ICN, information centric network, CCN, energy
Procedia PDF Downloads 32910216 Estimation of Transition and Emission Probabilities
Authors: Aakansha Gupta, Neha Vadnere, Tapasvi Soni, M. Anbarsi
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Protein secondary structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine and biotechnology. Some aspects of protein functions and genome analysis can be predicted by secondary structure prediction. This is used to help annotate sequences, classify proteins, identify domains, and recognize functional motifs. In this paper, we represent protein secondary structure as a mathematical model. To extract and predict the protein secondary structure from the primary structure, we require a set of parameters. Any constants appearing in the model are specified by these parameters, which also provide a mechanism for efficient and accurate use of data. To estimate these model parameters there are many algorithms out of which the most popular one is the EM algorithm or called the Expectation Maximization Algorithm. These model parameters are estimated with the use of protein datasets like RS126 by using the Bayesian Probabilistic method (data set being categorical). This paper can then be extended into comparing the efficiency of EM algorithm to the other algorithms for estimating the model parameters, which will in turn lead to an efficient component for the Protein Secondary Structure Prediction. Further this paper provides a scope to use these parameters for predicting secondary structure of proteins using machine learning techniques like neural networks and fuzzy logic. The ultimate objective will be to obtain greater accuracy better than the previously achieved.Keywords: model parameters, expectation maximization algorithm, protein secondary structure prediction, bioinformatics
Procedia PDF Downloads 47210215 Synthesis and Molecular Docking of Isonicotinohydrazide Derivatives as Anti-Tuberculosis Candidates
Authors: Ruswanto Ruswanto, Richa Mardianingrum, Tita Nofianti, Nur Rahayuningsih
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Tuberculosis (TB) is a chronic disease as a result of Mycobacterium tuberculosis. It can affect all age groups, and hence, is a global health problem that causes the death of millions of people every year. One of the drugs used in tuberculosis treatment is isonicotinohydrazide. In this study, N'-benzoylisonicotinohydrazide derivative compounds (a-l) were prepared using acylation reactions between isonicotinohydrazide and benzoyl chloride derivatives, through the reflux method. Molecular docking studies suggested that all of the compounds had better interaction with Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) than isonicotinohydrazide. It can be concluded that N'-benzoylisonicotinohydrazide derivatives (a-l) could be used as anti-tuberculosis candidates. From the docking results revealed that all of the compounds interact well with InhA, with compound g (N'-(3-nitrobenzoyl)isonicotinohydrazide) exhibiting the best interaction.Keywords: anti-tuberculosis , docking, InhA, N'-benzoylisonicotinohydrazide, synthesis
Procedia PDF Downloads 30110214 The Role of Situational Factors in User Experience during Human-Robot Interaction
Authors: Da Tao, Tieyan Wang, Mingfu Qin
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While social robots have been increasingly developed and rapidly applied in our daily life, how robots should interact with humans is still an urgent problem to be explored. Appropriate use of interactive behavior is likely to create a good user experience in human-robot interaction situations, which in turn can improve people’s acceptance of robots. This paper aimed to systematically and quantitatively examine the effects of several important situational factors (i.e., interaction distance, interaction posture, and feedback style) on user experience during human-robot interaction. A three-factor mixed designed experiment was adopted in this study, where subjects were asked to interact with a social robot in different interaction situations by combinations of varied interaction distance, interaction posture, and feedback style. A set of data on users’ behavioral performance, subjective perceptions, and eye movement measures were tracked and collected, and analyzed by repeated measures analysis of variance. The results showed that the three situational factors showed no effects on behavioral performance in tasks during human-robot interaction. Interaction distance and feedback style yielded significant main effects and interaction effects on the proportion of fixation times. The proportion of fixation times on the robot is higher for negative feedback compared with positive feedback style. While the proportion of fixation times on the robot generally decreased with the increase of the interaction distance, it decreased more under the positive feedback style than under the negative feedback style. In addition, there were significant interaction effects on pupil diameter between interaction distance and posture. As interaction distance increased, mean pupil diameter became smaller in side interaction, while it became larger in frontal interaction. Moreover, the three situation factors had significant interaction effects on user acceptance of the interaction mode. The findings are helpful in the underlying mechanism of user experience in human-robot interaction situations and provide important implications for the design of robot behavioral expression and for optimal strategies to improve user experience during human-robot interaction.Keywords: social robots, human-robot interaction, interaction posture, interaction distance, feedback style, user experience
Procedia PDF Downloads 12010213 Comparison of Different Artificial Intelligence-Based Protein Secondary Structure Prediction Methods
Authors: Jamerson Felipe Pereira Lima, Jeane Cecília Bezerra de Melo
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The difficulty and cost related to obtaining of protein tertiary structure information through experimental methods, such as X-ray crystallography or NMR spectroscopy, helped raising the development of computational methods to do so. An approach used in these last is prediction of tridimensional structure based in the residue chain, however, this has been proved an NP-hard problem, due to the complexity of this process, explained by the Levinthal paradox. An alternative solution is the prediction of intermediary structures, such as the secondary structure of the protein. Artificial Intelligence methods, such as Bayesian statistics, artificial neural networks (ANN), support vector machines (SVM), among others, were used to predict protein secondary structure. Due to its good results, artificial neural networks have been used as a standard method to predict protein secondary structure. Recent published methods that use this technique, in general, achieved a Q3 accuracy between 75% and 83%, whereas the theoretical accuracy limit for protein prediction is 88%. Alternatively, to achieve better results, support vector machines prediction methods have been developed. The statistical evaluation of methods that use different AI techniques, such as ANNs and SVMs, for example, is not a trivial problem, since different training sets, validation techniques, as well as other variables can influence the behavior of a prediction method. In this study, we propose a prediction method based on artificial neural networks, which is then compared with a selected SVM method. The chosen SVM protein secondary structure prediction method is the one proposed by Huang in his work Extracting Physico chemical Features to Predict Protein Secondary Structure (2013). The developed ANN method has the same training and testing process that was used by Huang to validate his method, which comprises the use of the CB513 protein data set and three-fold cross-validation, so that the comparative analysis of the results can be made comparing directly the statistical results of each method.Keywords: artificial neural networks, protein secondary structure, protein structure prediction, support vector machines
Procedia PDF Downloads 61210212 RNA Antisense Coat Protein Showing Promising Effects against Cotton Leaf Curl Disease in Pakistani Cotton
Authors: Zunnu Raen Akhtar
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Cotton Leaf Curl Disease (CLCuD) is from Gemini virus and is transmitted through whiteflies in cotton. Transgenic cotton containing Antisense Coat Protein (ACP) has been found to show better results against CLCuD in cotton. In current research, Antisense Coat Protein was inserted in cotton plants to observe resistance developed in the cotton plants against CLCuD. T1 generation of plants were observed for its expression in plants. Tests were carried out to observe the expression of Antisense Coat Protein using Polymerase Chain Reaction (PCR) technique and by southern blotting. Whiteflies showing positive Cotton Leaf Curl Virus (CLCV) were reared and released in bioassay on ACP expressing cotton plants under laboratory as well as confined semi-field conditions. Results confirmed the expression of AC protein in PCR and southern blotting. Further laboratory results showed that cotton plants expressing AC protein showed rare incidence of CLCuD infection as compared to control. In the confined semi-field, similar results were observed in AC protein expressing cotton as compared to control. These results explicitly show that ACP can help to tackle the CLCuD issue in the future and further studies on biochemical processes involved in these plants and effects of ACP induction on non-target organisms should also be studied for eco-system.Keywords: cotton, white flies, antisense coat protein, CLCV
Procedia PDF Downloads 17810211 Rational Design of Potent Compounds for Inhibiting Ca2+ -Dependent Calmodulin Kinase IIa, a Target of Alzheimer’s Disease
Authors: Son Nguyen, Thanh Van, Ly Le
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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking
Procedia PDF Downloads 26610210 The Effects of pH on p53 Phosphorylation by Ataxia Telangiectasia Mutated Kinase
Authors: Serap Pektas
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Ataxia telangiectasia mutated (ATM) is a serine-threonine kinase, which is the major regulator of the DNA damage response. ATM is activated upon the formation of DNA double-strand breaks (DSBs) in the cells. ATM phosphorylates the proteins involved in apoptotic responses, cell cycle checkpoint control, DNA repair, etc. Tumor protein p53, known as p53 is one of these proteins that phosphorylated by ATM. Phosphorylation of p53 at Ser15 residue leads to p53 stabilization in the cells. Often enzymes activity is affected by hydrogen ion concentration (pH). In order to find the optimal pH range for ATM activity, steady-state kinetic assays were performed at acidic and basic pH ranges. Ser15 phosphorylation of p53 is determined by using ELISA. The results indicated that the phosphorylation rate was better at basic pH range compared with the acidic pH range. This could be due to enzyme stability, or enzyme-substrate interaction is pH dependent.Keywords: ataxia telangiectasia mutated, DNA double strand breaks, DNA repair, tumor protein p53
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