Search results for: Millet protein concentrate

Authors: Kalyankumar M. Matti, Chandrashekhar J. Savanurmath, Shivayogeppa B. Hinchigeri

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A rare phenomenon of SDS-induced activation of a latent protease activity associated with the purified silkworm excretory red fluorescent protein (SE-RFP) was noticed. SE-RFP aliquots incubated with SDS for different time intervals indicated that the protein undergoes an obligatory breakdown into a number of subunits which exhibit autoproteolytic (acting upon themselves) and/or heteroproteolytic (acting on other proteins) activities. A strong serine protease activity of SE-RFP subunits on Bombyx mori nucleopolyhedrovirus (BmNPV) polyhedral protein was detected by zymography technique. A complete inhibition of BmNPV infection to silkworms was observed by the oral administration assay of the SE-RFP. Here, it is proposed that the SE-RFP prevents the initial infection of BmNPV to silkworms by obliterating the polyhedral protein. This is the first report on a silkworm red fluorescent protein that exhibits a protease activity on exposure to SDS. The present studies would help in understanding the antiviral mechanism of silkworm red fluorescent proteins.

Keywords: BmNPV, polyhedra, SE-RFP, SDS-induced protease activity, zymography.

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Authors: Pawel Glibowski, Agnieszka Glibowska

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The rheological properties, structure and potential synergistic interactions of whey proteins (1-6%) and inulin (20%) in mixed gels in the presence of CaCl2 was the aim of this study. Whey proteins have a strong influence on inulin gel formation. At low concentrations (2%) whey proteins did not impair in inulin gel formation. At higher concentration (4%) whey proteins impaired inulin gelation and inulin impaired the formation of a Ca2+-induced whey protein network. The presence of whey proteins at a level allowing for protein gel network formation (6%) significantly increased the rheological parameters values of the gels. SEM micrographs showed that whey protein structure was coated by inulin moieties which could make the mixed gels firmer. The protein surface hydrophobicity measurements did not exclude synergistic interactions between inulin and whey proteins, however. The use of an electrophoretic technique did not show any stable inulin-whey protein complexes.

Keywords: gels, hydrophobicity, inulin, SEM, whey proteins.

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Authors: R. Charoen, S. Tipkanon, W. Savedboworn, N. Phonsatta, A. Panya

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Rice bran protein hydrolysates (RBPH) were prepared from defatted rice bran of two different Thai rice cultivars (Plai-Ngahm-Prachinburi; PNP and Khao Dok Mali 105; KDM105) using an enzymatic method. This research aimed to optimize enzyme-assisted protein extraction. In addition, the functional properties of RBPH and their stabilities to environmental stresses including pH (3 to 8), ionic strength (0 mM to 500 mM) and the thermal treatment (30 °C to 90 °C) were investigated. Results showed that enzymatic process for protein extraction of defatted rice bran was as follows: enzyme concentration 0.075 g/ 5 g of protein, extraction temperature 50 °C and extraction time 4 h. The obtained protein hydrolysate powders had a degree of hydrolysis (%) of 21.05% in PNP and 19.92% in KDM105. The solubility of protein hydrolysates at pH 4-6 was ranged from 27.28-38.57% and 27.60-43.00% in PNP and KDM105, respectively. In general, antioxidant activities indicated by total phenolic content, FRAP, ferrous ion-chelating (FIC), and 2,2’-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) of KDM105 had higher than PNP. In terms of functional properties, the emulsifying activity index (EAI) was was 8.78 m²/g protein in KDM105, whereas PNP was 5.05 m²/g protein. The foaming capacity at 5 minutes (%) was 47.33 and 52.98 in PNP and KDM105, respectively. Glutamine, Alanine, Valine, and Leucine are the major amino acid in protein hydrolysates where the total amino acid of KDM105 gave higher than PNP. Furthermore, we investigated environmental stresses on the stability of 5% oil in water emulsion (5% oil, 10 mM citrate buffer) stabilized by RBPH (3.5%). The droplet diameter of emulsion stabilized by KDM105 was smaller (d < 250 nm) than produced by PNP. For environmental stresses, RBPH stabilized emulsions were stable at pH around 3 and 5-6, at high salt (< 400 mM, pH 7) and at temperatures range between 30-50°C.

Keywords: Functional properties, oil in water emulsion, protein hydrolysates, rice bran protein.

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Authors: S. Mousavian, D. Ashouri, F. Mousavian, V. Nikkhah Rashidabad, N. Ghazinia

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PH, temperature and time of extraction of each stage,  agitation speed and delay time between stages effect on efficiency of  zinc extraction from concentrate. In this research, efficiency of zinc  extraction was predicted as a function of mentioned variable by  artificial neural networks (ANN). ANN with different layer was  employed and the result show that the networks with 8 neurons in  hidden layer has good agreement with experimental data.

 

Keywords: Zinc extraction, Efficiency, Neural networks, Operating condition.

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Authors: C. Lanzerstorfer, M. Hinterberger

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The iron content of the ore used is crucial for the productivity and coke consumption rate in blast furnace pig iron production. Therefore, most iron ore deposits are processed in beneficiation plants to increase the iron content and remove impurities. In several comminution stages, the particle size of the ore is reduced to ensure that the iron oxides are physically liberated from the gangue. Subsequently, physical separation processes are applied to concentrate the iron ore. The fine-grained ore concentrates produced need to be transported, stored, and processed. For smooth operation of these processes, the flow properties of the material are crucial. The flowability of powders depends on several properties of the material: grain size, grain size distribution, grain shape, and moisture content of the material. The flowability of powders can be measured using ring shear testers. In this study, the influence of the moisture content on the flowability for the Krivoy Rog magnetite iron ore concentrate was investigated. Dry iron ore concentrate was mixed with varying amounts of water to produce samples with a moisture content in the range of 0.2 to 12.2%. The flowability of the samples was investigated using a Schulze ring shear tester. At all measured values of the normal stress (1.0 kPa – 20 kPa), the flowability decreased significantly from dry ore to a moisture content of approximately 3-5%. At higher moisture contents, the flowability was nearly constant, while at the maximum moisture content the flowability improved for high values of the normal stress only. The results also showed an improving flowability with increasing consolidation stress for all moisture content levels investigated. The wall friction angle of the dust with carbon steel (S235JR), and an ultra-high molecule low-pressure polyethylene (Robalon) was also investigated. The wall friction angle increased significantly from dry ore to a moisture content of approximately 3%. For higher moisture content levels, the wall friction angles were nearly constant. Generally, the wall friction angle was approximately 4° lower at the higher wall normal stress.

Keywords: Iron ore concentrate, flowability, moisture content, wall friction angle.

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Authors: N. Tuncbag, T. Haliloglu, O. Keskin

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Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: Mohammad Shoyaib, M. Abdullah-Al-Wadud, Oksam Chae

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Proteomics is one of the largest areas of research for bioinformatics and medical science. An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. Predicting Protein-Protein Interaction (PPI) is one of the crucial and decisive problems in current research. Genomic data offer a great opportunity and at the same time a lot of challenges for the identification of these interactions. Many methods have already been proposed in this regard. In case of in-silico identification, most of the methods require both positive and negative examples of protein interaction and the perfection of these examples are very much crucial for the final prediction accuracy. Positive examples are relatively easy to obtain from well known databases. But the generation of negative examples is not a trivial task. Current PPI identification methods generate negative examples based on some assumptions, which are likely to affect their prediction accuracy. Hence, if more reliable negative examples are used, the PPI prediction methods may achieve even more accuracy. Focusing on this issue, a graph based negative example generation method is proposed, which is simple and more accurate than the existing approaches. An interaction graph of the protein sequences is created. The basic assumption is that the longer the shortest path between two protein-sequences in the interaction graph, the less is the possibility of their interaction. A well established PPI detection algorithm is employed with our negative examples and in most cases it increases the accuracy more than 10% in comparison with the negative pair selection method in that paper.

Keywords: Interaction graph, Negative training data, Protein-Protein interaction, Support vector machine.

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Authors: Naruemon Prapasuwannakul

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Soymilk residue is obtained as a byproduct from soymilk and tofu production with little economic value. It contains high protein and fiber as well as various minerals and phyto-chemical compounds. The objective of this research was to substitute soymilk residue for wheat flour in gyoza skin in order to enhance value of soymilk residue and increase protein and fiber content of gyoza skin. Wheat flour was replaced with soymilk residue from 0 to 40%. The soy milk residue prepared in this research contains 26.92%protein, 3.58% fiber, 2.88% lipid, 6.29% ash and 60.33% carbohydrate. The results showed that increasing soymilk residue decreased lightness (L*value), tensile strength and sensory attributes but increased redness (a*), yellowness (b*), protein and fiber contents of product. The result also showed that the gyoza skin substituted with 30% soymilk residue was the most acceptable (p≤0.05) and its protein and fiber content increased up to 45 % and 867 % respectively.

Keywords: Gyoza skin, sensory, soymilk residue, wheat flour.

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Authors: Soichi Ogishima, Takeshi Hase, So Nakagawa, Yasuhiro Suzuki, Hiroshi Tanaka

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To understand life as biological system, evolutionary understanding is indispensable. Protein interactions data are rapidly accumulating and are suitable for system-level evolutionary analysis. We have analyzed yeast protein interaction network by both mathematical and biological approaches. In this poster presentation, we inferred the evolutionary birth periods of yeast proteins by reconstructing phylogenetic profile. It has been thought that hub proteins that have high connection degree are evolutionary old. But our analysis showed that hub proteins are entirely evolutionary new. We also examined evolutionary processes of protein complexes. It showed that member proteins of complexes were tend to have appeared in the same evolutionary period. Our results suggested that protein interaction network evolved by modules that form the functional unit. We also reconstructed standardized phylogenetic trees and calculated evolutionary rates of yeast proteins. It showed that there is no obvious correlation between evolutionary rates and connection degrees of yeast proteins.

Keywords: Protein interaction network, evolution, modularity, evolutionary rate, connection degrees.

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Authors: Marwa H. Mahmoud, Ferial M. Abu-Salem

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Soy protein is a common ingredient added to processed meats to enhance its functional characteristics. In our study, soybean products (fermented soy Natto and protein hydrolysate) containing hydrolyzed peptides and amino acids, with or without ascorbic acid were added to burger in order to improve its quality characteristics. Results showed that soy additives significantly increased moisture and protein content and reduced (P < 0.05) fat values. Ash content did not affect with Natto additive. Color tools, lightness and yellowness were higher (P<0.05) for the samples with added soybean products (with or without ascorbic acid), while redness decreased. Both of protein hydrolysate and ascorbic acid increased the softiness while, Natto additive increased the hardness of samples. Natto & protein hydrolysate additives increased the total volatile basic nitrogen while, samples with ascorbic acid decreased TVBN values at significant levels. Also, soy additives were improved both of cooking quality and sensory evaluation of the burger in order to prove that soy products actually affect the quality characteristics of meat products.

Keywords: Burger, protein hydrolysate, fermented soy Natto, quality characterization.

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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.

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Authors: Omar Gaci, Stefan Balev

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In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure.

Keywords: interaction network, protein structure, small-world network.

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Authors: Lubis A., Widayanti R., Hikmah Z., Endaryanto A., Harsono A., Harianto A., Etika R., Handayani D. K., Sampurna M.

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Neonatal lupus erythematous (NLE) is a rare disease marked by clinical characteristic and specific maternal autoantibody. Many cutaneous, cardiac, liver, and hematological manifestations could happen with affect of one organ or multiple. In this case, both babies were premature, low birth weight (LBW), small for gestational age (SGA) and born through caesarean section from a systemic lupus erythematous (SLE) mother. In the first case, we found a baby girl with dyspnea and grunting. Chest X ray showed respiratory distress syndrome (RDS) great I and echocardiography showed small atrial septal defect (ASD) and ventricular septal defect (VSD). She also developed anemia, thrombocytopenia, elevated C-reactive protein, hypoalbuminemia, increasing coagulation factors, hyperbilirubinemia, and positive blood culture of Klebsiella pneumonia. Anti-Ro/SSA and Anti-nRNP/sm were positive. Intravenous fluid, antibiotic, transfusion of blood, thrombocyte concentrate, and fresh frozen plasma were given. The second baby, male presented with necrotic tissue on the left ear and skin rashes, erythematous macula, athropic scarring, hyperpigmentation on all of his body with various size and facial haemorrhage. He also suffered from thrombocytopenia, mild elevated transaminase enzyme, hyperbilirubinemia, anti-Ro/SSA was positive. Intravenous fluid, methyprednisolone, intravenous immunoglobulin (IVIG), blood, and thrombocyte concentrate transfution were given. Two cases of neonatal lupus erythematous had been presented. Diagnosis based on clinical presentation and maternal auto antibody on neonate. Organ involvement in NLE can occur as single or multiple manifestations.

Keywords: Neonatus lupus erythematous, maternal autoantibody, clinical characteristic.

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Authors: Omima E. Fadlallah, Abdullahi H. El Tinay, Elfadil E. Babiker

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Sorghum flour was supplemented with 15 and 30% chickpea flour. Sorghum flour and the supplement were fermented at 35 oC for 0, 8, 16, and 24 h. Changes in pH, titrable acidity, total soluble solids, protein content, in vitro protein digestibility and amino acid composition were investigated during fermentation and/or after supplementation of sorghum flour with chickpea. The pH of the fermenting material decreased sharply with a concomitant increase in the titrable acidity. The total soluble solids remained unchanged with progressive fermentation time. The protein content of sorghum cultivar was found to be 9.27 and that of chickpea was 22.47%. The protein content of sorghum cultivar after supplementation with15 and 30% chickpea was significantly (P ≤ 0.05) increased to 11.78 and 14.55%, respectively. The protein digestibility also increased after fermentation from 13.35 to 30.59 and 40.56% for the supplements, respectively. Further increment in protein content and digestibility was observed when supplemented and unsupplemented samples were fermented for different periods of time. Cooking of fermented samples was found to increase the protein content slightly and decreased digestibility for both supplements. Amino acid content of fermented and fermented and cooked supplements was determined. Supplementation was found to increase the lysine and therionine content. Cooking following fermentation decreased lysine, isoleucine, valine and sulfur containg amino acids.

Keywords: Amino acid, Chickpea, Cooking, Fermentation, protein, Sorghum.

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Authors: Dilip Nath

Abstract:

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 in two phyla viz., Arthropods and Molluscs. Total ten 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

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Authors: Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu, Darby Tien-Hao Chang

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Search for a tertiary substructure that geometrically matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work, a web server has been built to predict protein-ligand binding sites based on automatically extracted templates. However, a drawback of such templates is that the web server was prone to resulting in many false positive matches. In this study, we present a sequence-order constraint to reduce the false positive matches of using automatically extracted templates to predict protein-ligand binding sites. The binding site predictor comprises i) an automatically constructed template library and ii) a local structure alignment algorithm for querying the library. The sequence-order constraint is employed to identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequence-order constraint can largely reduce the false positive matches and is effective for template-based binding site prediction.

Keywords: Protein structure, binding site, functional prediction

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

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The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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Authors: Jaruwan Chutrtong

Abstract:

This research aims to study consumer acceptance of Tempeh from various raw materials (type of bean) and determine protein contents for comparison. Tempeh made from soybean, peanut, white kidney bean and sesame in the ratio: - soybean:sesame =1:0.1, soybean:white kidney:sesame =1:1:0.1, soybean:peanut:sesame =1:1:0.1 and peanut:white kidney bean: sesame =1:1:0.1. The study found that consumer is most satisfied with appearances on soybean mixed with white kidney and black sesame tempeh (3.98). The most satisfied tempeh with textures is soybean mixed with peanut and black sesame tempeh (4.00). The most satisfied tempeh with odor is peanut mixed with white kidney bean and black sesame tempeh (4.04). And the most satisfied tempeh with flavor is peanut mixed with white kidney bean and black sesame tempeh (4.2). The amount of protein in production, soybean tempeh has the highest protein. When we add sesame seeds, it made the protein content slightly decreased (1.86 and 0.6 %). When we use peanut as raw material, the protein content decreased 15.3%. And when we use white kidney bean as raw material, the protein content decreased (22.77- 26.11%). 

Keywords: Acceptance, bean, protein content, tempeh.

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Authors: Ali Nouri Emamzadeh, Akbar Yaghobfar

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The experiment was conducted to evaluate digestibility quantities of protein in Canola Meals (CMs) between caecectomised and intact adult Rhode Island Red (RIR) cockerels with using conventional addition method (CAM) for 7 d: a 4-d adaptation and a 3-d experiment period on the basis of a completely randomized design with 4 replicates. Results indicated that caecectomy decreased (P<0.05) apparent and true digestibility quantities of protein for CMs, except for CMs 2 and 3. The mean apparent and true digestibility quantities for all CMs in caecectomised (80.5 and 81.4%, respectively) were (3.1 and 3.3%, respectively) less (P<0.05) than intact cockerels (83.6 and 84.7%, respectively). Therefore, the caecectomy method increases accuracy of the digestibility measurements of protein for this meal in bioassays based on excreta collection in adult cockerels.

Keywords: Adult cockerels, caecectomy, canola meals, proteindigestibility.

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Authors: J. Suwanprateeb, F. Thammarakcharoen

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Calcium phosphate coating (CaP) has been employed for protein delivery, but the typical direct protein adsorption on the coating led to low incorporation content and fast release of the protein from the coating. By using bovine serum albumin (BSA) as a model protein, rapid biomimetic co-precipitation between calcium phosphate and BSA was employed to control the distribution of BSA within calcium phosphate coating during biomimetic formation on titanium surface for only 6 h at 50oC in an accelerated calcium phosphate solution. As a result, the amount of BSA incorporation and release duration could be increased by using a rapid biomimetic coprecipitation technique. Up to 43 fold increases in the BSA incorporation content and the increase from 6 h to more than 360 h in release duration compared to typical direct adsorption technique were observed depending on the initial BSA concentration used during coprecipitation (1, 10 and 100 μg.ml-1). From x-ray diffraction and Fourier transform infrared spectroscopy studies, the coating composition was not altered with the incorporation of BSA by this rapid biomimetic co-precipitation and mainly comprised octacalcium phosphate and hydroxyapatite. However, the microstructure of calcium phosphate crystals changed from straight, plate-like units to curved, plate-like units with increasing BSA content.

Keywords: Biomimetic, Calcium Phosphate Coating, Protein, Titanium.

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Authors: Norzita Ngadi, John Abrahamson, Conan Fee, Ken Morison

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Poly (ethylene glycol) (PEG) molecules attached to surfaces have shown high potential as a protein repellent due to their flexibility and highly water solubility. A quartz crystal microbalance recording frequency and dissipation changes (QCM-D) has been used to study the adsorption from aqueous solutions, of lysozyme and α-lactalbumin proteins (the last with and without calcium) onto modified stainless steel surfaces. Surfaces were coated with poly(ethylene imine) (PEI) and silicate before grafting on PEG molecules. Protein adsorption was also performed on the bare stainless steel surface as a control. All adsorptions were conducted at 23°C and pH 7.2. The results showed that the presence of PEG molecules significantly reduced the adsorption of lysozyme and α- lactalbumin (with calcium) onto the stainless steel surface. By contrast, and unexpected, PEG molecules enhanced the adsorption of α-lactalbumin (without calcium). It is suggested that the PEG -α- lactalbumin hydrophobic interaction plays a dominant role which leads to protein aggregation at the surface for this latter observation. The findings also lead to the general conclusion that PEG molecules are not a universal protein repellent. PEG-on-PEI surfaces were better at inhibiting the adsorption of lysozyme and α-lactalbumin (with calcium) than with PEG-on-silicate surfaces.

Keywords: Stainless steel, PEG, QCM-D, protein, PEI layer, silicate layer.

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Authors: Ferial M. Abu-Salem, Marwa H. Mahmoud, M. H. El-Kalyoub, A. Y. Gibriel, Azza Abou-Arab

Abstract:

In order to characterize the soy protein hydrolysate obtained in this study, gel chromatography on Sephadex G-25 was used to perform the separation of the peptide mixture and electrophoresis in SDS-polyacrylamide gel has been employed. Protein hydrolysate gave high antioxidant activities, but didn't give any antimicrobial activities. The antioxidant activities of protein hydrolysate was in the same trend of peptide content which gave high antioxidant activities and high peptide content between fractions 15 to 50. With increasing peptide concentrations, the scavenging effect on DPPH radical increased until about 70%, thereafter reaching a plateau. In compare to different concentrations of BHA, which exhibited higher activity (90%), soybean protein hydrolysate exhibited high antioxidant activities (70%) at a concentration of 1.45 mg/ml at fraction 25. Electrophoresis analysis indicated that, low- MW hydrolysate fractions (F1) appeared, on average, to have higher DPPH scavenging activities than high-MW fractions. These results revealed that soybean peptides probably contain substances that were proton donors and could react with free radicals to convert them to stable diamagnetic molecules. 

Keywords: Antioxidant peptides, hydrolysis, protein hydrolysate, peptide fractions.

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Authors: Ji-Hyon Kil, Kew-Cheol Shim, Kyoung-Ae Park, Kyoungho Kim

Abstract:

Ambrosia trifida L. is designated as invasive alien species by the Act on the Conservation and Use of Biodiversity by the Ministry of Environment, Korea. The purpose of present paper was to investigate the inhibitory effects of aqueous extracts of A.trifida on the development of root hairs of Triticum aestivum L., and Allium tuberosum Rottler ex Spreng and the electrophoretic protein patterns of their radicles. The development of root hairs was inhibited by increasing of aqueous extract concentrations. Through SDS-PAGE, the electrophoretic protein bands of extracted proteins from their radicles were appeared in controls, but protein bands of specific molecular weight disappeared or weakened in treatments. In conclusion, inhibitory effects of A. trifida made two receptor species changed morphologically, and at the molecular level in early growth stage.

Keywords: Ambrosia trifida L., invasive alien species, inhibitory effect, root hair, electrophoretic protein, radicle.

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Authors: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: Zelmina Lubovac, Björn Olsson, Jonas Gamalielsson

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This paper describes a novel approach for deriving modules from protein-protein interaction networks, which combines functional information with topological properties of the network. This approach is based on weighted clustering coefficient, which uses weights representing the functional similarities between the proteins. These weights are calculated according to the semantic similarity between the proteins, which is based on their Gene Ontology terms. We recently proposed an algorithm for identification of functional modules, called SWEMODE (Semantic WEights for MODule Elucidation), that identifies dense sub-graphs containing functionally similar proteins. The rational underlying this approach is that each module can be reduced to a set of triangles (protein triplets connected to each other). Here, we propose considering semantic similarity weights of all triangle-forming edges between proteins. We also apply varying semantic similarity thresholds between neighbours of each node that are not neighbours to each other (and hereby do not form a triangle), to derive new potential triangles to include in module-defining procedure. The results show an improvement of pure topological approach, in terms of number of predicted modules that match known complexes.

Keywords: Modules, systems biology, protein interactionnetworks, yeast.

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Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

Abstract:

Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Dihydroxyacetone kinase, essential genes, Methicillin-resistant Staphylococcus aureus, drug target.

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Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

Abstract:

This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: Globular protein, modulating function, white noise, winding probability.

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Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

Abstract:

Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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Authors: Alireza Vakili, Mohsen Danesh Mesgaran, Majid Abdollazade

Abstract:

In this study four Holstein steers with rumen fistula fed 7 kg of dry matter (DM) of diets differing in concentrate to alfalfa hay ratios as 60:40, 70:30, 80:20, and 90:10 in a 4 × 4 latin square design. The pH of the ruminal fluid was measured before the morning feeding (0.0 h) to 8 h post feeding. In this study, a two-layered feed-forward neural network trained by the Levenberg-Marquardt algorithm was used for modelling of ruminal pH. The input variables of the network were time, concentrate to alfalfa hay ratios (C/F), non fiber carbohydrate (NFC) and neutral detergent fiber (NDF). The output variable was the ruminal pH. The modeling results showed that there was excellent agreement between the experimental data and predicted values, with a high determination coefficient (R2 >0.96). Therefore, we suggest using these model-derived biological values to summarize continuously recorded pH data.

Keywords: Ruminal pH, Artificial Neural Network (ANN), Non Fiber Carbohydrate, Neutral Detergent Fiber.

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Authors: Elaheh Jooybar, Mohammad J. Abdekhodaie, Marcel Karperien, Pieter J. Dijkstra

Abstract:

In this study, hyaluronic acid (HA) microgels were developed for the goal of protein delivery. First, a hyaluronic acid-tyramine conjugate (HA-TA) was synthesized with a degree of substitution of 13 TA moieties per 100 disaccharide units. Then, HA-TA microdroplets were produced using a water in oil emulsion method and crosslinked in the presence of horseradish peroxidase (HRP) and hydrogen peroxide (H₂O₂). Loading capacity and the release kinetics of lysozyme and BSA, as model proteins, were investigated. It was shown that lysozyme, a cationic protein, can be incorporated efficiently in the HA microgels, while the loading efficiency for BSA, as a negatively charged protein, is low. The release profile of lysozyme showed a sustained release over a period of one month. The results demonstrated that the HA-TA microgels are a good carrier for spatial delivery of cationic proteins for biomedical applications.

Keywords: Microgel, inverse emulsion, protein delivery, hyaluronic acid, crosslinking.

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