Search results for: degradability and synthesized microbial protein.

Authors: M. Jouki, N. Khazaei , A. Kalbasi , H. Tavakolipour, S. Rajabifar, F. Motamedi. Sedeh, A. Jouki

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Irradiation is considered one of the most efficient technological processes for the reduction of microorganisms in food. It can be used to improve the safety of food products, and to extend their shelf lives. The aim of this study was to evaluate the effects of gamma irradiation for improvement of saffron shelf life. Samples were treated with 0 (none irradiated), 1.0, 2.0, 3.0 and 4.0 kGy of gamma irradiation and held for 2 months. The control and irradiated samples were underwent microbial analysis, chemical characteristics and sensory evaluation at 30 days intervals. Microbial analysis indicated that irradiation had a significant effect (P < 0.05) on the reduction of microbial loads. There was no significant difference in sensory quality and chemical characteristics during storage in saffron.

Keywords: gamma irradiation, saffron, microbes, contamination.

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Authors: J. Elbl, J. K. Friedel, J. Záhora, L. Plošek, A. Kintl, J. Přichystalová, J. Hynšt, L. Dostálová, K. Zákoutská

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This work presents the first results from the long-term experiment, which is focused on the impact of intensive rainfall and long period of drought on microbial activities in soil. Fifteen lysimeters were prepared in the area of our interest. This area is a protection zone of underground source of drinking water. These lysimeters were filed with topsoil and subsoil collected in this area and divided into two groups. These groups differ in fertilization and amount of water received during the growing season. Amount of microbial biomass and leaching of mineral nitrogen and phosphates were chosen as main indicators of microbial activities in soil. Content of mineral nitrogen and phosphates was measured in soil solution, which was collected from each lysimeters. Amount of microbial biomass was determined in soil samples that were taken from the lysimeters before and after the long period of drought and intensive rainfall.

Keywords: Mineral nitrogen, Phosphates, Microbial activities, Drought, Precipitation.

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Authors: Chun-Wei Tung, Chyn Liaw, Shinn-Jang Ho, Shinn-Ying Ho

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Protein subchloroplast locations are correlated with its functions. In contrast to the large amount of available protein sequences, the information of their locations and functions is less known. The experiment works for identification of protein locations and functions are costly and time consuming. The accurate prediction of protein subchloroplast locations can accelerate the study of functions of proteins in chloroplast. This study proposes a Random Forest based method, ChloroRF, to predict protein subchloroplast locations using interpretable physicochemical properties. In addition to high prediction accuracy, the ChloroRF is able to select important physicochemical properties. The important physicochemical properties are also analyzed to provide insights into the underlying mechanism.

Keywords: Chloroplast, Physicochemical properties, Proteinlocations, Random Forests.

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Authors: Supanun Kangrang, Kraipat Cheenkachorn, Kittiphong Rattanaporn, Malinee Sriariyanun

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Rice straw is lignocellulosic biomass which can be utilized as substrate for the biogas production. However, due to the property and composition of rice straw, it is difficult to be degraded by hydrolysis enzymes. One of the pretreatment methods that modify such properties of lignocellulosic biomass is the application of lignocellulose-degrading microbial consortia. The aim of this study is to investigate the effect of microbial consortia to enhance biogas production. To select the high efficient consortium, cellulase enzymes were extracted and their activities were analyzed. The results suggested that microbial consortium culture obtained from cattle manure is the best candidate compared to decomposed wood and horse manure. A microbial consortium isolated from cattle manure was then mixed with anaerobic sludge and used as inoculum for biogas production. The optimal conditions for biogas production were investigated using response surface methodology (RSM). The tested parameters were the ratio of amount of microbial consortium isolated and amount of anaerobic sludge (MI:AS), substrate to inoculum ratio (S:I) and temperature. Here, the value of the regression coefficient R2 = 0.7661 could be explained by the model which is high to advocate the significance of the model. The highest cumulative biogas yield was 104.6 ml/g-rice straw at optimum ratio of MI:AS, ratio of S:I, and temperature of 2.5:1, 15:1 and 44°C respectively.

Keywords: Lignocellulolytic biomass, microbial consortium, cellulase, biogas, Response Surface Methodology.

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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: N. Khazaei, M. Jouki, A. Kalbasi, H. Tavakolipour, S. Rajabifar, F. Motamedi. Sedeh, A. Jouki

Abstract:

In this research saffron samples were prepared from farms and sampling was done in four states contain : sampling from fresh saffron of petal with forceps , sampling from fresh saffron of petal by hands, sampling from dried sample by warm air in shadow, sampling from dried sample which dried by dryer. Samples collected and kept in sterile tubes and containers and carried to laboratory and maintained until experiment. Microbial experiments were performed to determine microbial load such as total count, Staphylococcus aureus, coli form, E.coli, mold and yeast. Results showed that in picking and drying stages the contamination amount increases in saffron samples. There was a significant difference between the microbial load of picked up saffron by forceps and by hands, and also between dried saffron by warm air in shadow and by dryer.

Keywords: saffron; contaminations; preparation method

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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: 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: Ö. Öztürk, O. Şaman

Abstract:

Sesame is one of the oldest and most important oil crops as main crop and second crop agriculture. This study was carried out to determine the effects of different inter- and intra-row spacings on the yield and yield components on second crop sesame; was set up in Antalya West Mediterranean Agricultural Research Institue in 2009. Muganlı 57 sesame cultivar was used as plant material. The field experiment was set up in a split plot design and row spacings (30, 40, 50, 60 and 70 cm) were assigned to the main plots and and intra-row spacings (5, 10, 20 and 30 cm) were assigned to the subplots. Seed yield, oil ratio, oil yield, protein ratio and protein yield were investigated. In general, wided inter row spacings and intra-row spacings, resulted in decreased seed yield, oil yield and protein yield. The highest seed yield, oil yield and protein yield (respectively, 1115.0 kg ha-1, 551.3 kg ha-1, 224.7 kg ha-1) were obtained from 30x5 cm plant density while the lowest seed yield, oil yield and protein yield (respectively, 677.0 kg ha-1, 327.0 kg ha-1, 130.0 kg ha-1) were recorded from 70x30 cm plant density. As a result, in terms of oil yield for second crop sesame agriculture, 30 cm row spacing, and 5 cm intra row spacing are the most suitable plant densities.

Keywords: Sesamum indicum L., oil ratio, oil yield, protein ratio, protein yield

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

Abstract:

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: Kessara Seneesrisakul, Erdogan Gulari, Sumaeth Chavadej

Abstract:

The complex structure of lignocellulose leads to great difficulties in converting it to fermentable sugars for the ethanol production. The major hydrolysis impediments are the crystallinity of cellulose and the lignin content. To improve the efficiency of enzymatic hydrolysis, microbial pretreatment of corncob was investigated using two bacterial strains of Bacillus subtilis A 002 and Cellulomonas sp. TISTR 784 (expected to break open the crystalline part of cellulose) and lignin-degrading fungus, Phanerochaete sordida SK7 (expected to remove lignin from lignocellulose). The microbial pretreatment was carried out with each strain under its optimum conditions. The pretreated corncob samples were further hydrolyzed to produce reducing glucose with low amounts of commercial cellulase (25 U·g-1 corncob) from Aspergillus niger. The corncob samples were determined for composition change by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and scanning electron microscope (SEM). According to the results, the microbial pretreatment with fungus, P. sordida SK7 was the most effective for enhancing enzymatic hydrolysis, approximately, 40% improvement.

Keywords: Corncob, Enzymatic hydrolysis, Microorganisms, Pretreatment.

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Authors: Sunil Dehipawala, Gayathrie Amarasuriya, N. Gadura, G. Tremberger Jr, D. Lieberman, Harry Gafney, Todd Holden, T. Cheung

Abstract:

The iron environment in Fe-doped Vycor Anode was investigated with EXAFS using Brookhaven Synchrotron Light Source. The iron-reducing Shewanella oneidensis culture was grown in a microbial fuel cell under anaerobic respiration. The Fe bond length was found to decrease and correlate with the amount of biofilm growth on the Fe-doped Vycor Anode. The data suggests that Fe-doped Vycor Anode would be a good substrate to study the Shewanella oneidensis nanowire structure using EXAFS.

Keywords: EXAFS, Fourier Transform, Microbial Fuel Cell, Shewanella oneidensis.

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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: Javier Sánchez, Laura Elena De León Prado, Dora Alicia Cortés Hernández

Abstract:

Magnetic spinel ferrites are materials that possess size, magnetic properties and heating ability adequate for their potential use in biomedical applications. The Mn_0.5Ga_0.5Fe₂O₄ magnetic nanoparticles (MNPs) were synthesized by sol-gel method using citric acid as chelating agent of metallic precursors. The synthesized samples were identified by X-Ray Diffraction (XRD) as an inverse spinel structure with no secondary phases. Saturation magnetization (Ms) of crystalline powders was 45.9 emu/g, which was higher than those corresponding to GaFe₂O₄ (14.2 emu/g) and MnFe₂O₄ (40.2 emu/g) synthesized under similar conditions, while the coercivity field (Hc) was 27.9 Oe. The average particle size was 18 ± 7 nm. The heating ability of the MNPs was enough to increase the surrounding temperature up to 43.5 °C in 7 min when a quantity of 4.5 mg of MNPs per mL of liquid medium was tested. Cytotoxic effect (hemolysis assay) of MNPs was determined and the results showed hemolytic values below 1% in all tested cases. According to the results obtained, these synthesized nanoparticles can be potentially used as thermoseeds for hyperthermia therapy.

Keywords: Cytotoxicity, heating ability, manganese-gallium ferrite, magnetic hyperthermia.

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

Abstract:

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: Jayesh M. Sonawane, Prakash C. Ghosh

Abstract:

Landfill leachate emerges as a promising feedstock for microbial fuel cells (MFCs). In the present investigation, direct air-breathing cathode-based MFCs are fabricated to investigate the potential of landfill leachate. Three MFCs that have different cathode areas are fabricated and investigated for 17 days under open circuit conditions. The maximum open circuit voltage (OCV) is observed to be as high as 1.29 V. The maximum cathode area specific power density achieved in the reactor is 1513 mW m^-2. Further studies are under progress to understand the origin of high OCV obtained from landfill leachate-based MFCs.

Keywords: Microbial fuel cells, landfill leachate, air-breathing cathode, performance study.

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Authors: Naruemon Prapasuwannakul

Abstract:

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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