Search results for: Globular protein

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

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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: Sudarat Jiamyangyuen, Tipawan Thongsook, Riantong Singanusong, Chanida Saengtubtim

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Rice bran is normally used as a raw material for rice bran oil production or sold as feed with a low price. Conventionally, the protein in defatted rice bran was extracted using alkaline extraction and acid precipitation, which involves in chemical usage and lowering some nutritious component. This study was conducted in order to extract of rice bran protein concentrate (RBPC) from defatted rice bran using enzymes and employing polysaccharides in a precipitating step. The properties of RBPC obtained will be compared to those of a control sample extracted using a conventional method. The results showed that extraction of protein from rice bran using enzymes exhibited the higher protein recovery compared to that extraction with alkaline. The extraction conditions using alcalase 2% (v/w) at 50 C, pH 9.5 gave the highest protein (2.44%) and yield (32.09%) in extracted solution compared to other enzymes. Rice bran protein concentrate powder prepared by a precipitation step using alginate (protein in solution: alginate 1:0.016) exhibited the highest protein (27.55%) and yield (6.84%). Precipitation using alginate was better than that of acid. RBPC extracted with alkaline (ALK) or enzyme alcalase (ALC), then precipitated with alginate (AL) (samples RBP-ALK-AL and RBP-ALC-AL) yielded the precipitation rate of 75% and 91.30%, respectively. Therefore, protein precipitation using alginate was then selected. Amino acid profile of control sample, and sample precipitated with alginate, as compared to casein and soy protein isolated, showed that control sample showed the highest content among all sample. Functional property study of RBP showed that the highest nitrogen solubility occurred in pH 8-10. There was no statically significant between emulsion capacity and emulsion stability of control and sample precipitated by alginate. However, control sample showed a higher of foaming capacity and foaming stability compared to those of sample precipitated with alginate. The finding was successful in terms of minimizing chemicals used in extraction and precipitation steps in preparation of rice bran protein concentrate. This research involves in a production of value-added product in which the double amount of protein (28%) compared to original amount (14%) contained in rice bran could be beneficial in terms of adding to food products e.g. healthy drink with high protein and fiber. In addition, the basic knowledge of functional property of rice bran protein concentrate was obtained, which can be used to appropriately select the application of this value-added product from rice bran.

Keywords: Alginate, carrageenan, rice bran, rice bran protein.

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

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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

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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 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

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

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

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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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Authors: Zarmina Gillani, Nuzhat Huma, Aysha Sameen, Mulazim Hussain Bukhari

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Whey is an excellent food ingredient owing to its high nutritive value and its functional properties. However, composition of whey varies depending on composition of milk, processing conditions, processing method, and its whey protein content. The aim of this study was to prepare a whey powder from raw whey and to determine the influence of different processing temperatures (160 and 180 °C) on the physicochemical, functional properties during storage of 180 days and on whey protein denaturation. Results have shown that temperature significantly (P < 0.05) affects the pH, acidity, non-protein nitrogen (NPN), protein total soluble solids, fat and lactose contents. Significantly (p < 0.05) higher foaming capacity (FC), foam stability (FS), whey protein nitrogen index (WPNI), and a lower turbidity and solubility index (SI) were observed in whey powder processed at 160 °C compared to whey powder processed at 180 °C. During storage of 180 days, slow but progressive changes were noticed on the physicochemical and functional properties of whey powder. Reverse phase-HPLC analysis revealed a significant (P < 0.05) effect of temperature on whey protein contents. Denaturation of β-Lactoglobulin is followed by α-lacalbumin, casein glycomacropeptide (CMP/GMP), and bovine serum albumin (BSA).

Keywords: Whey powder, temperature, denaturation, reverse phase – HPLC.

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Authors: Marios Poulos, Eirini Maliagani, Minas Paschopoulos, George Bokos

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The purpose of my research proposal is to demonstrate that there is a relationship between EEG and endometrial cancer. The above relationship is based on an Aristotelian Syllogism; since it is known that the 14-3-3 protein is related to the electrical activity of the brain via control of the flow of Na+ and K+ ions and since it is also known that many types of cancer are associated with 14-3-3 protein, it is possible that there is a relationship between EEG and cancer. This research will be carried out by well-defined diagnostic indicators, obtained via the EEG, using signal processing procedures and pattern recognition tools such as neural networks in order to recognize the endometrial cancer type. The current research shall compare the findings from EEG and hysteroscopy performed on women of a wide age range. Moreover, this practice could be expanded to other types of cancer. The implementation of this methodology will be completed with the creation of an ontology. This ontology shall define the concepts existing in this research-s domain and the relationships between them. It will represent the types of relationships between hysteroscopy and EEG findings.

Keywords: Bioinformatics, Protein 14-3-3, EEG, Endometrial cancer, Ontology.

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Authors: S. Ashrafpour, T. Tohidi Moghadam, B. Ranjbar

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Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 μM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme- AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.

Keywords: Nanocarrier, Nanoparticles, Surface Plasmon Resonance, Quenching Fluorescence.

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Authors: Patrick Nwabueze Okechukwu, Ima Nirwana Soelaiman, Gabriele Anisah Ruth Froemming, Mohd Yusri Idorus, Norazlina Mohamed

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Supplementation of palm vitamin E has been reported to prevent loss of bone density in ovariectomised female rats. The mechanism by which palm vitamin E exerts these effects is still unknown. We hypothesized that palm vitamin E may act by preventing the protein expression changes. Two dimensional poly acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software genomic solutions Investigator (proteomics) was used to analyze the differential protein expression profile in femoral and humeri bones harvested from three groups of rats; sham-operated rats (SO), ovariectomised rats (Ovx) and ovariectomised rats supplemented for 2 months with palm vitamin E. The results showed that there were over 300 valued spot on each of the groups PVE and OVX as compared to about 200 in SO. Comparison between the differential protein expression between OVX and PVE groups showed that ten spots were down –regulated in OVX but up-regulated in PVE. The ten differential spots were separately named P1-P10. The identification and understanding of the pathway of the differential protein expression among the groups is ongoing and may account for the molecular mechanism through which palm vitamin E exert its anti-osteoporotic effect.

Keywords: Palm vitamin E, ovariectomised, osteoporosis protein expression, 2-d-page.

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Authors: Norlin Pauzi, Ahmad R.M. Yahya, Zairossani Nor, Amirul A. Abdullah

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Strain M was isolated from the latex of Hevea brasiliensis that grow in the rubber farm area of Malaysia Rubber Board. Strain M was tentatively identified as Bacillus sp. Strain M demonstrated high protease production at pH 9, and this was suitable to be applied in rubber processing that was in alkaline conditions. The right and suitable proportion to be used in applying supernatant into the latex was two parts of latex and one part of enzyme. In this proportion, the latex was stable throughout the 72 hours of treatment. The potential of strain M to degrade protein in the natural rubber latex was proven with the reduction of 79.3% nitrogen in 24 hours treatment. Centrifugation process of the latex before undergoing the treatment had increased the protein degradation in latex. Although the centrifugation process did not achieve zero nitrogen content, it had improved the performance of protein denaturing in the natural rubber.

Keywords: Hevea brasiliensis, Bacillus sp., protease, latex.

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Authors: Vita Strazdina, Aleksandrs Jemeljanovs, Vita Sterna

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Not all proteins have the same nutritional value, since protein quality strongly depends on its amino acid composition and digestibility. The meat of game animals could be a high protein source because of its well-balanced essential amino acids composition. Investigations about biochemical composition of game meat such as wild boar (Sus scrofa scrofa), roe deer (Capreolus capreolus) and beaver (Castor fiber) are not very much. Therefore, the aim of the investigation was evaluate protein composition of game meat hunted in Latvia. The biochemical analysis, evaluation of connective tissue and essential amino acids in meat samples were done, the amino acids score were calculate. Results of analysis showed that protein content 20.88-22.05% of all types of meat samples is not different statistically. The content of connective tissue from 1.3% in roe deer till 1.5% in beaver meat allowed classified game animal as high quality meat. The sum of essential amino acids in game meat samples were determined 7.05–8.26g100g-1. Roe deer meat has highest protein content and lowest content of connective tissues among game meat hunted in Latvia. Concluded that amino acid score for limiting amino acids phenylalanine and tyrosine is high and shows high biological value of game meat.

Keywords: Dietic product, game meat, amino acids, scores.

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Authors: Anna Trusek-Holownia, Andrzej Noworyta

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Using an enzyme of known specificity the hydrolysis of protein was carried out in a controlled manner. The aim was to obtain oligopeptides being the so-called active peptides or their direct precursors. An original way of expression of the protein hydrolysis kinetics was introduced. Peptide bonds contained in the protein were recognized as a diverse-quality substrate for hydrolysis by the applied protease. This assumption was positively verified taking as an example the hydrolysis of albumin by thermolysin. Peptide linkages for this system should be divided into at least four groups. One of them is a group of bonds non-hydrolyzable by this enzyme. These that are broken are hydrolyzed at a rate that differs even by tens of thousands of times. Designated kinetic constants were k'_F = 10991.4 L/g^.h, k'_M = 14.83L/g^.h, k'_S about 10^-1 L/g^.h for fast, medium and slow bonds, respectively. Moreover, a procedure for unfolding of the protein, conducive to the improved susceptibility to enzymatic hydrolysis (approximately three-fold increase in the rate) was proposed.

Keywords: Peptide bond hydrolysis, kinetics, enzyme specificity, biologically active peptides.

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Authors: Xiaoli Shen, Yuehui Chen

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Interactions among proteins are the basis of various life events. So, it is important to recognize and research protein interaction sites. A control set that contains 149 protein molecules were used here. Then 10 features were extracted and 4 sample sets that contained 9 sliding windows were made according to features. These 4 sample sets were calculated by Radial Basis Functional neutral networks which were optimized by Particle Swarm Optimization respectively. Then 4 groups of results were obtained. Finally, these 4 groups of results were integrated by decision fusion (DF) and Genetic Algorithm based Selected Ensemble (GASEN). A better accuracy was got by DF and GASEN. So, the integrated methods were proved to be effective.

Keywords: protein interaction sites, features, sliding windows, radial basis functional neutral networks, genetic algorithm basedselected ensemble.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

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Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: G. Lavanya Devi, Allam Appa Rao, A. Damodaram, GR Sridhar, G. Jaya Suma

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Cluster analysis divides data into groups that are meaningful, useful, or both. Analysis of biological data is creating a new generation of epidemiologic, prognostic, diagnostic and treatment modalities. Clustering of protein sequences is one of the current research topics in the field of computer science. Linear relation is valuable in rule discovery for a given data, such as if value X goes up 1, value Y will go down 3", etc. The classical linear regression models the linear relation of two sequences perfectly. However, if we need to cluster a large repository of protein sequences into groups where sequences have strong linear relationship with each other, it is prohibitively expensive to compare sequences one by one. In this paper, we propose a new technique named General Regression Model Technique Clustering Algorithm (GRMTCA) to benignly handle the problem of linear sequences clustering. GRMT gives a measure, GR*, to tell the degree of linearity of multiple sequences without having to compare each pair of them.

Keywords: Clustering, General Regression Model, Protein Sequences, Similarity Measure.

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Authors: Fiona Browne, Huiru Zheng, Haiying Wang, Francisco Azuaje

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Recent years have seen a growing trend towards the integration of multiple information sources to support large-scale prediction of protein-protein interaction (PPI) networks in model organisms. Despite advances in computational approaches, the combination of multiple “omic" datasets representing the same type of data, e.g. different gene expression datasets, has not been rigorously studied. Furthermore, there is a need to further investigate the inference capability of powerful approaches, such as fullyconnected Bayesian networks, in the context of the prediction of PPI networks. This paper addresses these limitations by proposing a Bayesian approach to integrate multiple datasets, some of which encode the same type of “omic" data to support the identification of PPI networks. The case study reported involved the combination of three gene expression datasets relevant to human heart failure (HF). In comparison with two traditional methods, Naive Bayesian and maximum likelihood ratio approaches, the proposed technique can accurately identify known PPI and can be applied to infer potentially novel interactions.

Keywords: Bayesian network, Classification, Data integration, Protein interaction networks.

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Authors: Gry M, Bergström J, Lengquist J, Lindberg J, Drobin K, Schwenk J, Nilsson P, Schuppe-Koistinen I.

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Sensitive and predictive DILI (Drug Induced Liver Injury) biomarkers are needed in drug R&D to improve early detection of hepatotoxicity. The discovery of DILI biomarkers that demonstrate the predictive power to identify individuals at risk to DILI would represent a major advance in the development of personalized healthcare approaches. In this healthy volunteer acetaminophen study (4g/day for 7 days, with 3 monitored nontreatment days before and 4 after), 450 serum samples from 32 subjects were analyzed using protein profiling by antibody suspension bead arrays. Multiparallel protein profiles were generated using a DILI target protein array with 300 antibodies, where the antibodies were selected based on previous literature findings of putative DILI biomarkers and a screening process using pre dose samples from the same cohort. Of the 32 subjects, 16 were found to develop an elevated ALT value (2Xbaseline, responders). Using the plasma profiling approach together with multivariate statistical analysis some novel findings linked to lipid metabolism were found and more important, endogenous protein profiles in baseline samples (prior to treatment) with predictive power for ALT elevations were identified.

Keywords: DILI, Plasma profiling, PLSDA, Randomforest.

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Authors: B. Bina, M.H. Mehdinejad, Gunnel Dalhammer, Guna RajaraoM. Nikaeen, H. Movahedian Attar

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Coagulation of water involves the use of coagulating agents to bring the suspended matter in the raw water together for settling and the filtration stage. Present study is aimed to examine the effects of aluminum sulfate as coagulant in conjunction with Moringa Oleifera Coagulant Protein as coagulant aid on turbidity, hardness, and bacteria in turbid water. A conventional jar test apparatus was employed for the tests. The best removal was observed at a pH of 7 to 7.5 for all turbidities. Turbidity removal efficiency was resulted between % 80 to % 99 by Moringa Oleifera Coagulant Protein as coagulant aid. Dosage of coagulant and coagulant aid decreased with increasing turbidity. In addition, Moringa Oleifera Coagulant Protein significantly has reduced the required dosage of primary coagulant. Residual Al+3 in treated water were less than 0.2 mg/l and meets the environmental protection agency guidelines. The results showed that turbidity reduction of % 85.9- % 98 paralleled by a primary Escherichia coli reduction of 1-3 log units (99.2 – 99.97%) was obtained within the first 1 to 2 h of treatment. In conclusions, Moringa Oleifera Coagulant Protein as coagulant aid can be used for drinking water treatment without the risk of organic or nutrient release. We demonstrated that optimal design method is an efficient approach for optimization of coagulation-flocculation process and appropriate for raw water treatment.

Keywords: MOCP, Coagulant aid, turbidity removal, E.coliremoval, water, treatment

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Authors: Shahram Naghizadeh Raeisi, Ali Alghooneh

Abstract:

Using membrane technology and modification of milk protein structural properties, a lactose free yogurt was developed. The functional, textural and structural properties of the sample were evaluated and compared with the commercial ones. Results showed that the modification of protein in high fat set yogurt resulted in 11.55%, 18%, 20.21% and 7.08% higher hardness, consistency, water holding capacity, and shininess values compared with the control one. Furthermore, these indices of modified low fat set yogurt were 21.40%, 25.41%, 28.15% & 10.58% higher than the control one, which could be related to the gel network microstructural properties in yogurt formulated with modified protein. In this way, in comparison with the control one, the index of linkage strength (A), the number of linkages (z), and time scale of linkages (λrel) of the high fat modified yogurt were 22.10%, 50.68%, 21.82% higher than the control one; whereas, the average linear distance between two adjacent crosslinks (ξ), was 16.77% lower than the control one. For low fat modified yogurt, A, z, λrel, and ξ indices were 34.30%, 61.70% and 42.60% higher and 19.20% lower than the control one, respectively. The shelf life of modified yogurt was extended to 10 weeks in the refrigerator, while, the control set yogurt had a 3 weeks shelf life. The acidity of high fat and low fat modified yogurts increased from 76 to 84 and 72 to 80 Dornic degrees during 10 weeks of storage, respectively, whereas for control high fat and low fat yogurts they increased from 82 to 122 and 77 to 112 Dornic degrees, respectively. This behavior could be due to the elimination of microorganism’s source of energy in modified yogurt. Furthermore, the calories of high fat and low fat lactose free yogurts were 25% and 40% lower than their control samples, respectively. Generally, results showed that the lactose free yogurt with modified protein, despite of 1% lower protein content than the control one, showed better functional properties, nutritional properties, network parameters, and shelf stability, which could be promising in the set yogurt industry.

Keywords: Lactose free, low calorie, network properties, protein modification.

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Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

Abstract:

In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrinrepeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number oftransmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.

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Authors: Tom Snir, Eitan Rubin

Abstract:

Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.

Keywords: Systems Biology, Protein Length

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Authors: B. Coşgun, Ö. Öztürk

Abstract:

Canola is a specific edible type of rapeseed, developed in the 1970s, which contains about 40 percent oil. This research was carried out to determine the yield and some quality characteristics of some winter canola cultivars during the 2010-2011 vegetation period in Central Anatolia of Turkey. In this research; Oase, Dante, Californium, Excalibur, Elvis, ES Hydromel, Licord, Orkan, Vectra, Nelson, Champlain and NK Petrol winter canola varieties were used as material. The field experiment was set up in a “Randomized Complete Block Design” with three replications on 21 September 2010. In this research; seed yield, oil content, protein content, oil yield and protein yield were examined. As a result of this research; seed yield, oil content, oil yield and protein yield (except protein content) were significant differences between the cultivars. The highest seed yield (6348 kg ha-1) was obtained from the NK Petrol, while the lowest seed yield (3949 kg ha-1) was determined from the Champlain cultivar was obtained. The highest oil content (46.73%) was observed from Oase and the lowest value was obtained from Vectra (41.87%) cultivar. The highest oil yield (2950 kg ha-1) was determined from NK Petrol while the least value (1681 kg ha-1) was determined from Champlain cultivar. The highest protein yield (1539.3 kg ha-1) was obtained from NK Petrol and the lowest protein yield (976.5 kg ha-1) was obtained from Champlain cultivar. The main purpose of the cultivation of oil crops, to increase the yield of oil per unit area. According the result of this research, NK Petrol cultivar which ranks first with regard to both seed yield and oil yield between cultivars as the most suitable winter canola cultivar of local conditions.

Keywords: Cultivar, Oil yield, Rapeseed, Seed Yield.

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Authors: Fawzi Irshaid, Fatiha Dilmi, Khaled Tarawneh, Raji Hadeth, Adnan Jaran, Ahad Al-Khatib

Abstract:

P16/INK4A is tumor suppressor protein that plays a critical role in cell cycle regulation. Loss of P16 protein expression has been implicated in pathogenesis of many cancers, including lymphoma. Therefore, we sought to investigate if loss of P16 protein expression is associated with lymphoma and/or any specific lymphoma subtypes (Hodgkin-s lymphoma (HL) and nonHodgkin-s lymphoma (NHL)). Fifty-five lymphoma cases consisted of 30 cases of HL and 25 cases of NHL, with an age range of 3 to 78 years, were examined for loss of P16 by immunohistochemical technique using a specific antibody reacting against P16. In total, P16 loss was seen in 33% of all lymphoma cases. P16 loss was identified in 47.7% of HL cases. In contrast, only 16% of NHL showed loss of P16. Loss of P16 was seen in 67% of HL patients with 50 years of age or older, whereas P16 loss was found in only 42% of HL patients with less than 50 years of age. P16 loss in HL is somewhat higher in male (55%) than in female (30%). In subtypes of HL, P16 loss was found exclusively in all cases of lymphocyte depletion, lymphocyte predominance and unclassified cases, whereas P16 loss was seen in 39% of mixed cellularity and 29% of nodular sclerosis cases. In low grade NHL patients, P16 loss was seen in approximately one-third of cases, whereas no or very rare of P16 loss was found in intermediate and high grade cases. P16 loss did not show any correlation with age or gender of NHL patients. In conclusion, the high rate of P16 loss seen in our study suggests that loss of P16 expression plays a critical role in the pathogenesis of lymphoma, particularly with HL.

Keywords: B-cells, immunostaining, P16 protein, Reed-Sternberg cells, tumors.

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Authors: Olufunke O. Ezekiel, Ogugua C. Aworh

Abstract:

Solid state fermentation of cassava peel with emphasis on protein enrichment using Trichoderma viride was evaluated. The effect of five variables: moisture content, pH, particle size (p), nitrogen source and incubation temperature; on the true protein and total sugars of cassava peel was investigated. The optimum fermentation period was established to be 8 days. Total sugars were 5-fold higher at pH 6 relative to pH 4 and 7-fold higher when cassava peels were fermented at 30oC relative to 25oC as well as using ammonium sulfate as the nitrogen source relative to urea or a combination of both. Total sugars ranged between 123.21mg/g at 50% initial moisture content to 374mg/g at 60% and from 190.59mg/g with particle size range of 2.00>p>1.41mm to 310.10mg/g with 4.00>p>3.35mm.True protein ranged from 229.70 mg/g at pH 4 to 284.05 mg/g at pH 6; from 200.87 mg/g with urea as nitrogen source and to 254.50mg/g with ammonium sulfate; from 213.82mg/g at 50% initial moisture content to 254.50mg/g at 60% moisture content, from 205.75mg/g in cassava peel with 5.6>p> 4.75mm to 268.30 in cassava peel with particle size 4.00>p>3.35mm, from 207.57mg/g at 25oC to 254.50mg/g at 30oC Cassava peel with particle size 4.00>p>3.35 mm and initial moisture content of 60% at pH 6.0, 30oC incubation temperature with ammonium sulfate (10g N / kg substrate) was most suitable for protein enrichment with Trichoderma viride. Crude protein increased from 4.21 % in unfermented cassava peel samples to 10.43 % in fermented samples.

Keywords: Cassava peel, Solid state fermentation, Trichoderma viride, Total sugars, True protein.

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