Search results for: protein quality

Authors: Do Phuc, Nguyen Thi Kim Phung

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In this paper, we represent protein structure by using graph. A protein structure database will become a graph database. Each graph is represented by a spectral vector. We use Jacobi rotation algorithm to calculate the eigenvalues of the normalized Laplacian representation of adjacency matrix of graph. To measure the similarity between two graphs, we calculate the Euclidean distance between two graph spectral vectors. To cluster the graphs, we use M-tree with the Euclidean distance to cluster spectral vectors. Besides, M-tree can be used for graph searching in graph database. Our proposal method was tested with graph database of 100 graphs representing 100 protein structures downloaded from Protein Data Bank (PDB) and we compare the result with the SCOP hierarchical structure.

Keywords: Eigenvalues, m-tree, graph database, protein structure, spectra graph theory.

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Authors: Majid Toghyani, Abbas Ali Gheisari, Ali Khodami, Mehdi Toghyani, Mohammad Mohammadrezaei, Ramin Bahadoran

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This experiment was conducted to investigate the effect of different levels of dietary chromium yeast (Cr-yeast) on thigh meat quality of broiler chicks reared under heat stress condition. Two hundred and forty Ross male chickens in heat stress condition (33±3°C) were allocated to five treatments in a completely randomized design. Treatments were supplemented with 0 (control), 200, 400, 800 and 1200 μg kg-1 Cr in the form of Cr yeast. Twelve chicks from each treatment were slaughtered at 42 d, to evaluate moisture, protein, lipid, pH and lipid oxidation of thigh meat. Protein, moisture, lipid and pH of thigh meat were not affected by supplemental Cr. Thigh meat lipid tended to decrease in broilers received 1200 μg kg-1. Storage time increased lipid oxidation of meat (P<0.01). Lipid oxidation of thigh muscle for two days of storage were affected by supplemental Cr and decreased (P<0.05). Results of this study showed that dietary Cr-yeast supplementation improved the thigh meat quality of broiler chicks in heat stress condition.

Keywords: Broiler, Heat stress, Chromium yeast, Thigh meat quality.

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Authors: Omar GACI, Stefan BALEV, Antoine DUTOT

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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 observe that according to their structural roles, the nodes interact differently. By leading a community structure detection, we confirm this specific behavior and describe thecommunities composition to finally propose a new approach to fold a protein interaction network.

Keywords: interaction network, protein structure, community structure detection.

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Authors: Chan Weng Howe, Mohd Saberi Mohamad

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Protein residue contact map is a compact representation of secondary structure of protein. Due to the information hold in the contact map, attentions from researchers in related field were drawn and plenty of works have been done throughout the past decade. Artificial intelligence approaches have been widely adapted in related works such as neural networks, genetic programming, and Hidden Markov model as well as support vector machine. However, the performance of the prediction was not generalized which probably depends on the data used to train and generate the prediction model. This situation shown the importance of the features or information used in affecting the prediction performance. In this research, support vector machine was used to predict protein residue contact map on different combination of features in order to show and analyze the effectiveness of the features.

Keywords: contact map, protein residue contact, support vector machine, protein structure prediction

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Authors: Manpreet Singh, Parvinder Singh Sandhu, Reet Kamal Kaur

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Protein structure determination and prediction has been a focal research subject in the field of bioinformatics due to the importance of protein structure in understanding the biological and chemical activities of organisms. The experimental methods used by biotechnologists to determine the structures of proteins demand sophisticated equipment and time. A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results. However, prediction accuracies of these methods rarely exceed 70%.

Keywords: Protein, Secondary Structure, Prediction, DNA, RNA.

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Authors: Omer Nebil Yaveroglu, Tolga Can

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In this study, a high accuracy protein-protein interaction prediction method is developed. The importance of the proposed method is that it only uses sequence information of proteins while predicting interaction. The method extracts phylogenetic profiles of proteins by using their sequence information. Combining the phylogenetic profiles of two proteins by checking existence of homologs in different species and fitting this combined profile into a statistical model, it is possible to make predictions about the interaction status of two proteins. For this purpose, we apply a collection of pattern recognition techniques on the dataset of combined phylogenetic profiles of protein pairs. Support Vector Machines, Feature Extraction using ReliefF, Naive Bayes Classification, K-Nearest Neighborhood Classification, Decision Trees, and Random Forest Classification are the methods we applied for finding the classification method that best predicts the interaction status of protein pairs. Random Forest Classification outperformed all other methods with a prediction accuracy of 76.93%

Keywords: Protein Interaction Prediction, Phylogenetic Profile, SVM , ReliefF, Decision Trees, Random Forest Classification

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

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Nonspecific protein adsorption generally occurs on any solid surfaces and usually has adverse consequences. Adsorption of proteins onto a solid surface is believed to be the initial and controlling step in biofouling. Surfaces modified with end-tethered poly(ethylene glycol) (PEG) have been shown to be protein-resistant to some degree. In this study, the adsorption of β-casein and lysozyme was performed on 6 different types of surfaces where PEG was tethered onto stainless steel by polyethylene imine (PEI) through either OH or NHS end groups. Protein adsorption was also performed on the bare stainless steel surface as a control. The adsorption was conducted at 23 °C and pH 7.2. In situ QCM-D was used to determine PEG adsorption kinetics, plateau PEG chain densities, protein adsorption kinetics and plateau protein adsorbed quantities. PEG grafting density was the highest for a NHS coupled chain, around 0.5 chains / nm2. Interestingly, lysozyme which has smaller size than β-casein, appeared to adsorb much less mass than that of β- casein. Overall, the surface with high PEG grafting density exhibited a good protein rejection.

Keywords: QCM-D, PEG, stainless steel, β-casein, lysozyme.

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Authors: Rania A. Abul Seoud, Nahed H. Solouma, Abou-Baker M. Youssef, Yasser M. Kadah

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Due to the ever growing amount of publications about protein-protein interactions, information extraction from text is increasingly recognized as one of crucial technologies in bioinformatics. This paper presents a Protein Interaction Extraction System using a Link Grammar Parser from biomedical abstracts (PIELG). PIELG uses linkage given by the Link Grammar Parser to start a case based analysis of contents of various syntactic roles as well as their linguistically significant and meaningful combinations. The system uses phrasal-prepositional verbs patterns to overcome preposition combinations problems. The recall and precision are 74.4% and 62.65%, respectively. Experimental evaluations with two other state-of-the-art extraction systems indicate that PIELG system achieves better performance. For further evaluation, the system is augmented with a graphical package (Cytoscape) for extracting protein interaction information from sequence databases. The result shows that the performance is remarkably promising.

Keywords: Link Grammar Parser, Interaction extraction, protein-protein interaction, Natural language processing.

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Authors: N. Namviriyachote, N. Bang, P. Aramwit

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Silk sericin (SS) is a glue-like protein from silkworm cocoon. With its outstanding moisturization and activation collagen synthesis properties, silk protein is applied for wound healing. Since wound dressing in film preparation can facilitate patients- convenience and reduce risk of wound contraction, SS and polyvinyl alcohol (PVA) films were prepared with various concentrations of SS. Their physical properties such as surface density, light transmission, protein dissolution and tensile modulus were investigated. The results presented that 3% SS with 2% PVA is the best ingredient for SS film forming.

Keywords: Sericin, silk protein, film, wound healing.

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Authors: Laima Silina, Ilze Gramatina, Liga Skudra, Tatjana Rakcejeva

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The aim of the current research was to determine quality parameters changes of dried venison during storage. Protein, fat and moisture content dynamics as well microbiological quality was analyzed. For the experiments the meat (0.02×4.00×7.00 cm) pieces were marinated in “teriyaki sauce” marinade (composition: teriyaki sauce, sweet and sour sauce, taco sauce, soy sauce, American BBQ sauce hickory, sesame oil, garlic, garlic salt, tabasco red pepper sauce) at 4±2°C temperature for 48±1h. Sodium monophosphate (E339) was also added in part of marinade to improve the meat textural properties. After marinating, meat samples were dried in microwave-vacuum drier MUSSON–1, packaged in vacuum pouches made from polymer film (PA/PE) with barrier properties and storage for 4 months at 18±1°C temperature in dark place. Dried venison samples were analyzed after 0, 35, 91 and 112 days of storage. During the storage total plate counts of dried venison samples significantly (p<0.05) increased. No significant differences in the content of protein, fat and moisture were detected when analyzing dried meat samples during storage and comparing them with the chemical parameters of just dried meat.

Keywords: Drying, microwave-vacuum drier, quality, venison.

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Authors: Zurinahni Zainol, Rosalina Abdul Salam, Rosni Abdullah, Nur'Aini, Wahidah Husain

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The size, complexity and number of databases used for protein information have caused bioinformatics to lag behind in adapting to the need to handle this distributed information. Integrating all the information from different databases into one database is a challenging problem. Our main research is to develop a tool which can be used to access and manipulate protein information from difference databases. In our approach, we have integrated difference databases such as Swiss-prot, PDB, Interpro, and EMBL and transformed these databases in flat file format into relational form using XML and Bioperl. As a result, we showed this tool can search different sizes of protein information stored in relational database and the result can be retrieved faster compared to flat file database. A web based user interface is provided to allow user to access or search for protein information in the local database.

Keywords: Protein sequence database, relational database, integrated database.

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Authors: Ibrahim A. Akasha, Lydia Campbell, Stephen R. Euston

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Date palm (Phoenix dactylifera L.) seeds are waste streams which are considered a major problem to the food industry. They contain potentially useful protein (10-15% of the whole date-s weight). Global production, industrialisation and utilisation of dates are increasing steadily. The worldwide production of date palm fruit has increased from 1.8 million tons in 1961 to 6.9 million tons in 2005, thus from the global production of dates are almost 800.000 tonnes of date palm seeds are not currently used [1]. The current study was carried out to convert the date palm seeds into useful protein powder. Compositional analysis showed that the seeds were rich in protein and fat 5.64 and 8.14% respectively. We used several laboratory scale methods to extract proteins from seed to produce a high protein powder. These methods included simple acid or alkali extraction, with or without ultrafiltration and phenol trichloroacetic acid with acetone precipitation (Ph/TCA method). The highest protein content powder (68%) was obtained by Ph/TCA method with yield of material (44%) whereas; the use of just alkali extraction gave the lowest protein content of 8%, and a yield of 32%.

Keywords: Date palm seed, Phoenix dactylifera L., extraction of date palm seed protein

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Authors: A. F. Ali, D. M. Shawky

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Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.

Keywords: Bioinformatics, Artificial Neural Networks, Protein Sequence Analysis, Feature Extraction.

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Authors: Liene Strauta, Sandra Muizniece-Brasava, Ina Alsina

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Phaseolus coccineus L. is the third most important cultivated Phaseolus species in the world. It is widely grown in Latvia due to its earliness, good taste and uniform and qualitative yield. Experiments were carried out in the laboratories of Department of Food Technology and Agronomical Analysis Scientific Laboratory at Latvia Universityof Agriculture. Beans (Phaseolus coccineus L.) crude protein, crude ash content as well as colour measurements were analyzed. Results show, that brown coloured beans have less crude protein content than others, and ash content have significant differences.

Keywords: Phaseoluscoccineus, protein, ash, colour.

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Authors: Eszter Tóth, Ervin Welker

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Shadoo protein (Sho) was described in 2003 as the newest member of Prion protein superfamily [1]. Sho has similar structural motifs like prion protein (PrP) that is known for its central role in transmissible spongiform enchephalopathies. Although a great number of functions have been proposed, the exact physiological function of PrP is not known yet. Investigation of the function and localization of Sho may help us to understand the function of the Prion protein superfamily. Analyzing the subcellular localization of YFP-tagged forms of Sho, we detected the protein in the plasma membrane and in the nucleus of various cell lines. To reveal the localization of the endogenous protein we generated antibodies against Shadoo as well as employed commercially available anti-Shadoo antibodies: i) EG62 anti-mouse Shadoo antibody generated by Eurogentec Ltd.; ii) S-12 anti-human Shadoo antibody by Santa Cruz Biotechnology Inc.; iii) R-12 anti-mouse Shadoo antibody by Santa Cruz Biotechnology Inc.; iv) SPRN antibody against human Shadoo by Abgent Inc. We carried out immunocytochemistry on non-transfected HeLa, Zpl 2-1, Zw 3-5, GT1-1, GT1-7 and SHSY5Y cells as well as on YFP-Sho, Sho-YFP, and YFP-GPI transfected HeLa cells. Their specificity (in antibody-peptide competition assay) and co-localization (with the YFP signal) were assessed.

Keywords: Shadoo, prion protein, immunocytochemistry, antibody-peptide competition assay, antibody.

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Authors: F. M. Abu-Salem, M. H. Mahmoud, M. H. El-Kalyoubi, A. Y. Gibriel, A. A. Abou-Arab Arab

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Dried soy protein hydrolysate powder was added to the burger in order to enhance the oxidative stability as well as decreases the microbial spoilage. The soybean bioactive compounds (soy protein hydrolysate) as antioxidant and antimicrobial were added at level of 1, 2 and 3 %.Chemical analysis and physical properties were affected by protein hydrolysate addition. The TBA values were significantly affected (P < 0.05) by the storage period and the level of soy protein hydrolysate. All the tested soybean protein hydrolysate additives showed strong antioxidant properties. Samples of soybean protein hydrolysate showed the lowest (P < 0.05) TBA values at each time of storage. The counts of all determined microbiological indicators were significantly (P < 0.05) affected by the addition of the soybean protein hydrolysate. Decreasing trends of different extent were also observed in samples of the treatments for total viable counts, Coliform, Staphylococcus aureus, yeast and molds. Storage period was being significantly (P < 0.05) affected on microbial counts in all samples Staphylococcus aureus were the most sensitive microbe followed by Coliform group of the sample containing protein hydrolysate, while molds and yeast count showed a decreasing trend but not significant (P < 0.05) until the end of the storage period compared with control sample. Sensory attributes were also performed, added protein hydrolysate exhibits beany flavor which was clear about samples of 3% protein hydrolysate.

Keywords: Antioxidant, antimicrobial, isoflavones, bioactive peptide, antioxidant peptides, soybean protein hydrolysate.

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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: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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Authors: Mohamed A. Ahmed, Lydia J. Campbell

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The fortified of soft wheat flour with cowpea flour in bread making was investigated. The Soft wheat flour (SWF) was substituted by cowpea flour at levels of 5, 15 and 20%. The protein content of composite breads ranged from 6.1 – 9.9%. Significant difference was observed in moisture, protein and crude fibre contents of control (wheat bread) and composite bread at 5% addition of cowpea. Water absorption capacities of composite flours increased with increasing levels of cowpea flour in the blend. The specific loaf volume decreased significantly with increased cowpea content of blends. The overall acceptability of the 5% cowpea flour content of composite bread was not significantly different from the control (Soft Wheat-bread) but there is significantly different with increasing the levels of cowpea flour in the blend more than 5%.

Keywords: Cowpea flour, wheat flour, baking properties, sensory quality.

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Authors: ElShazali A. Mohamed, Isam A. Mohamed Ahmed, Elfadil E. Babiker

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This work describes refrigeration effects during storage on total protein and amino acids composition of raw and processed flour of two pearl millet cultivars (Ashana and Dembi). The protein content of the whole raw flour was found to be 14.46 and 13.38% for Ashana and Dembi cultivars, respectively. Dehulling of the grains reduced the protein content to 13.38 and 12.67% for the cultivars, respectively. For both cultivars, the protein content of the whole and dehulled raw flour before and after cooking was slightly decreased when the flour was stored for 60 days even after refrigeration. The effect of refrigeration process in combination with the storage period, cooking or dehulling was found to be vary between amino acids and even between cultivars. Regardless of the storage period and processing method, the amino acids content was remained unchanged after refrigeration for both cultivars.

Keywords: Amino acids, dehulling, Irradiation, Millet, protein content.

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Authors: Athanasios T. Alexiou, Maria M. Psiha, John A. Rekkas, Panayiotis M. Vlamos

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Mitochondria are dynamic organelles, capable to interact with each other. While the number of mitochondria in a cell varies, their quality and functionality depends on the operation of fusion, fission, motility and mitophagy. Nowadays, several researches declare as an important factor in neurogenerative diseases the disruptions in the regulation of mitochondrial dynamics. In this paper a stochastic model in BioAmbients calculus is presented, concerning mitochondrial fusion and its distribution in the renewal of mitochondrial population in a cell. This model describes the successive and dependent stages of protein synthesis, protein-s activation and merging of two independent mitochondria.

Keywords: Mitochondrial Dynamics, P-Calculus, StochasticModeling.

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

Abstract:

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

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

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Authors: Payel Ghosh, Rama Chandra Pradhan, Sabyasachi Mishra

Abstract:

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

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

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

Abstract:

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

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

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