Search results for: proteins

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

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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: Fatma N. Talkhan, H. H. Abo-Assy, K. A. Soliman, Marwa M. Azzam, A. Z. E. Abdelsalam, A. S. Abdel-Razek

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The Egyptian Bacillus thuringiensis isolate (M5) produce crystal proteins that is toxic against insects was irradiated with UV light to induce mutants. Upon testing 10 of the resulting mutants for their toxicity against cotton leafworm larvae, the three mutants 62, 64 and 85 proved to be the most toxic ones. Upon testing these mutants along with their parental isolate by SDS-PAGE analysis of spores-crystals proteins as well as vegetative cells proteins, new induced bands appeared in the three mutants by UV radiation and also they showed disappearance of some other bands as compared with the wild type isolate. Multiplex PCR technique, with five sets of specific primers, was used to detect the three types of cryI genes cryIAa, cryIAb and cryIAc. Results showed that these three genes exist, as distinctive bands, in the wild type isolate (M5) as well as in mutants 62 and 85, while the mutant 64 had two distinctive bands of cryIAb and cryIAc genes, and a faint band of cryI Aa gene. Finally, these results revealed that mutant 62 is considered as the promising mutant since it is UV resistant, highly toxic against Spodoptera littoralis and active against a wide range of Lepidopteran insects.

Keywords: Bacillus thuringiensis, biological control, cry1 genes, multiplex PC, SDS- PAGE analysis.

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Authors: Tom Snir, Eitan Rubin

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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: 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: Razvan Bocu, Sabin Tabirca

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The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents a new technique that allows for an accurate analysis of the human interactome network. It is basically a two-step analysis process that involves, at first, the detection of each protein-s absolute importance through the betweenness centrality computation. Then, the second step determines the functionallyrelated communities of proteins. For this purpose, we use a community detection technique that is based on the edge betweenness calculation. The new technique was thoroughly tested on real biological data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its experimental usefulness, the novel technique is also computationally effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented and a possible optimization solution for cancer drugs design is suggested.

Keywords: Betweenness centrality, interactome networks, proteinprotein interactions, protein communities, cancer.

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Authors: M. Hashemi, R. Madani, N. Razmi

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M. paratuberculosis is a slow growing mycobactin dependent mycobacterial species known to be the causative agent of Johne’s disease in all species of domestic ruminants worldwide. JD is characterized by gradual weight loss; decreased milk production. Excretion of the organism may occur for prolonged periods (1 to 2.5 years) before the onset of clinical disease. In recent years researchers focus on identification a specific antigen of MAP to use in diagnosis test and preparation of effective vaccine. In this paper, for production of polyclonal antibody against proteins of Mycobacterium avium paratuberculosis cell well a rabbit immunization at a certain time period with antigen. After immunization of the animal, rabbit was bleeded for producing enriched serum. Antibodies were purification with ion exchange chromatography. For exact measurement of interaction, western blotting test was used that this study demonstrated sharp bands appears in nitrocellulose paper and specific bands were 50 and 150 KD molecular weight. These were indicating immunodominant proteins.

Keywords: Paratuberculosis, Immunodominant, Western blotting, Ion exchange choromatography.

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Authors: Nahid A. Ali, Salma H. Ahmed, ElShazali A. Mohamed, Isam A. Mohamed Ahmed, Elfadil E.Babiker

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The effect of cross linking of the protein isolates of three legumes with the microbial enzyme transglutaminase (EC 2.3.2.13) on the functional properties at different NaCl concentration was studied. The reduction in the total free amino groups (OD340) of the polymerized protein showed that TGase treatment cross-linking the protein subunit of each legume. The solubility of the protein polymer of each legume was greatly improved at high concentration of NaCl. At 1.2 M NaCl the solubility of the native legumes protein was significantly decreased but after polymerization slightly improved. Cross linked proteins were less turbid on heating to higher temperature as compared to native proteins and the temperature at which the protein turns turbid also increased in the polymerized proteins. The emulsifying and foaming properties of the protein polymer were greatly improved at all concentrations of NaCl for all legumes.

Keywords: Functional properties, Legumes, Protein isolate, NaCl, Transglutaminase.

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Authors: John R. Rose, James P. Cleveland, Alvin Fox

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Tandem mass spectrometry (MS/MS) is the engine driving high-throughput protein identification. Protein mixtures possibly representing thousands of proteins from multiple species are treated with proteolytic enzymes, cutting the proteins into smaller peptides that are then analyzed generating MS/MS spectra. The task of determining the identity of the peptide from its spectrum is currently the weak point in the process. Current approaches to de novo sequencing are able to compute candidate peptides efficiently. The problem lies in the limitations of current scoring functions. In this paper we introduce the concept of proteome signature. By examining proteins and compiling proteome signatures (amino acid usage) it is possible to characterize likely combinations of amino acids and better distinguish between candidate peptides. Our results strongly support the hypothesis that a scoring function that considers amino acid usage patterns is better able to distinguish between candidate peptides. This in turn leads to higher accuracy in peptide prediction.

Keywords: Tandem mass spectrometry, proteomics, scoring, peptide, de novo, mutual information

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

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Understanding proteins functions is a major goal in the post-genomic era. Proteins usually work in context of other proteins and rarely function alone. Therefore, it is highly relevant to study the interaction partners of a protein in order to understand its function. Machine learning techniques have been widely applied to predict protein-protein interactions. Kernel functions play an important role for a successful machine learning technique. Choosing the appropriate kernel function can lead to a better accuracy in a binary classifier such as the support vector machines. In this paper, we describe a Bayesian kernel for the support vector machine to predict protein-protein interactions. The use of Bayesian kernel can improve the classifier performance by incorporating the probability characteristic of the available experimental protein-protein interactions data that were compiled from different sources. In addition, the probabilistic output from the Bayesian kernel can assist biologists to conduct more research on the highly predicted interactions. The results show that the accuracy of the classifier has been improved using the Bayesian kernel compared to the standard SVM kernels. These results imply that protein-protein interaction can be predicted using Bayesian kernel with better accuracy compared to the standard SVM kernels.

Keywords: Bioinformatics, Protein-protein interactions, Bayesian Kernel, Support Vector Machines.

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Authors: Chia-Ta Tsai, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Shinn-Ying Ho

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Prediction of bacterial virulent protein sequences can give assistance to identification and characterization of novel virulence-associated factors and discover drug/vaccine targets against proteins indispensable to pathogenicity. Gene Ontology (GO) annotation which describes functions of genes and gene products as a controlled vocabulary of terms has been shown effectively for a variety of tasks such as gene expression study, GO annotation prediction, protein subcellular localization, etc. In this study, we propose a sequence-based method Virulent-GO by mining informative GO terms as features for predicting bacterial virulent proteins. Each protein in the datasets used by the existing method VirulentPred is annotated by using BLAST to obtain its homologies with known accession numbers for retrieving GO terms. After investigating various popular classifiers using the same five-fold cross-validation scheme, Virulent-GO using the single kind of GO term features with an accuracy of 82.5% is slightly better than VirulentPred with 81.8% using five kinds of sequence-based features. For the evaluation of independent test, Virulent-GO also yields better results (82.0%) than VirulentPred (80.7%). When evaluating single kind of feature with SVM, the GO term feature performs much well, compared with each of the five kinds of features.

Keywords: Bacterial virulence factors, GO terms, prediction, protein sequence.

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Authors: P. Konvalina, I. Capouchová, Z. Stehno

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The organic farmers use wider range of crop varieties than the conventional farming. Bread wheat is the most favorite and the most common food crop. The organic bread wheat is usually of worse technological quality. Therefore, it is supposed to be an attractive alternative to the hulled wheat species (einkorn, emmer wheat and spelt). Twenty-five hulled bread wheat varieties and control bread wheat ones were grown on the certified organic parcel in České Budějovice (the Czech Republic) between 2009 and 2012. Their baking quality was measured and evaluated with standard methods, and in accordance with ICC. The results have shown that the grain of hulled wheat varieties contain a lot of proteins in grains (up to 18 percent); even the organic hulled bread wheat varieties are characterized by such good baking quality. Einkorn and emmer wheat are of worse technological quality of proteins (low values of gluten index and Zeleny test), which is a disadvantage of these two wheat species. On the other hand, spelt wheat is of better technological quality and is similar to the control bread wheat varieties. Mixtures consisting of bread wheat, among others, are considered good alternatives; they may contribute to wider range of use of the hulled wheat species. It is one of the possibilities which may increase the proportion of proteins in bread wheat grains; the nutrition-rich hulled wheat grains may be also used in such way at the same time.

Keywords: Baking quality, organic farming, einkorn, emmer wheat, spelt.

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Authors: Hanina M. N., Hairul Shahril M., Mohd Fazrullah Innsan M. F., Ismatul Nurul Asyikin I., Abdul Jalil A. K, Salina M. R., Ahmad I.B.

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Proteins levels produced by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antimicrobial agents or antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics or natural compounds in nature as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was focusing on the effect of essential oils from Cymbopogon flexuosus and C. nardus in regulating proteins production by Bacillus subtilis ATCC 21332. The Minimum Inhibition Concentrations (MICs) of both essential oils on B. subtilis were determined by using microdilution assay, resulting 0.2% and 1.56% for each C. flexuosus and C. nardus subsequently. The bacteria were further exposed to each essential oils at concentration of 0.01XMIC for 2 days. The proteins were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Protein profile showed that a band with approximate size of 250 kD was appeared for the treated bacteria with essential oils. Thus, Bacillus subtilis ATCC 21332 in stressful condition with the presence of essential oils at low concentration could induce the protein production.

Keywords: Bacillus subtilis ATCC 21332, Cymbopogon essential oils, protein

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Authors: Abu Salim Mustafa

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The comparisons of mycobacterial genomes have identified several Mycobacterium tuberculosis-specific genomic regions that are absent in other mycobacteria and are known as regions of differences. Due to M. tuberculosis-specificity, the peptides encoded by these regions could be useful in the specific diagnosis of tuberculosis. To explore this possibility, overlapping synthetic peptides corresponding to 39 proteins predicted to be encoded by genes present in regions of differences were tested for antibody-reactivity with sera from tuberculosis patients and healthy subjects. The results identified four immunodominant peptides corresponding to four different proteins, with three of the peptides showing significantly stronger antibody reactivity and rate of positivity with sera from tuberculosis patients than healthy subjects. The fourth peptide was recognized equally well by the sera of tuberculosis patients as well as healthy subjects. Predication of antibody epitopes by bioinformatics analyses using ABCpred server predicted multiple linear epitopes in each peptide. Furthermore, peptide sequence analysis for sequence identity using BLAST suggested M. tuberculosis-specificity for the three peptides that had preferential reactivity with sera from tuberculosis patients, but the peptide with equal reactivity with sera of TB patients and healthy subjects showed significant identity with sequences present in nob-tuberculous mycobacteria. The three identified M. tuberculosis-specific immunodominant peptides may be useful in the serological diagnosis of tuberculosis.

Keywords: Genomic regions of differences, Mycobacterium tuberculosis, peptides, serodiagnosis.

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Authors: Essam Al-Daoud

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A New features are extracted and compared to improve the prediction of protein-protein interactions. The basic idea is to select and use the best set of features from the Tensor matrices that are produced by the frequency vectors of the protein sequences. Three set of features are compared, the first set is based on the indices that are the most common in the interacting proteins, the second set is based on the indices that tend to be common in the interacting and non-interacting proteins, and the third set is constructed by using random indices. Moreover, three encoding strategies are compared; that are based on the amino asides polarity, structure, and chemical properties. The experimental results indicate that the highest accuracy can be obtained by using random indices with chemical properties encoding strategy and support vector machine.

Keywords: protein-protein interactions, random indices, encoding strategies, support vector machine.

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Authors: Bahareh Hajirostamloo

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Recent research has shown that milk proteins can yield bioactive peptides with opioid, mineral binding, cytomodulatory, antihypertensive, immunostimulating, antimicrobial and antioxidative activity in the human body. Bioactive peptides are encrypted in milk proteins and are only released by enzymatic hydrolysis in vivo during gastrointestinal digestion, food processing or by microbial enzymes in fermented products. At present significant research is being undertaken on the health effects of bioactive peptides. A variety of naturally formed bioactive peptides have been found in fermented dairy products, such as yoghurt, sour milk and cheese. In particular, antihypertensive peptides have been identified in fermented milks, whey and ripened cheese. Some of these peptides have been commercialized in the form of fermented milks. Bioactive peptides have the potential to be used in the formulation of health-enhancing nutraceuticals, and as potent drugs with well defined pharmacological effects.

Keywords: Milk protein, Bioactive peptides, Health effects, Dairy product.

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Authors: Orose Rugchati, Kanita Thanacharoenchanaphas

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This research studied the simulation of increased ambient ozone to estimate nutrient content and genetic changes in two Thai soybean cultivars (Chiang Mai 60 and Srisumrong 1). Ozone stress conditions affected proteins and lipids. It was found that proteins decreased, but lipids increased. Srisumrong 1 cultivars were more sensitive to ozone stress than Chiang Mai 60 cultivars. The effect of ozone stress conditions on plant phenotype and genotype was analyzed using the AFLP technique for the 2 Thai soybean cultivars (Chiang Mai 60 and Srisumrong 1).

Keywords: simulation, ambient ozone estimate, nutrient content, genetic changes , Thai soybean

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Authors: P. Grasgruber, J. Cacek, S. Hřebíčková

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The purpose of this study was to test the reliability of various standards that assess the quality of proteins via the “amino-acid score” and serve as a nutritional guideline for both children and adults. The height of young men in 42 European countries, Australia, New Zealand and USA was compared with the average consumption of food (after FAOSTAT, 2009) and a subsequent statistical analysis identified types of food with the most pronounced effect on physical growth. The results show that milk products and pork meat are by far the most significant nutritional factors in this regard. Cereals, vegetables and especially wheat played a strongly negative role. The results generally agreed best with the amino-acid score of proteins according to the standard of FAO 1985. In our opinion, the new standard of FAO 2007 underestimates the importance of tryptophan, which should provoke a debate about new modifications of the FAO guidelines.

Keywords: Protein quality, amino-acid score, physical growth, male height.

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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: Yahia M., Laanani I., Benbia S., Hachemi M., Massinissa Y.

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Uterine and oviducal fluids are necessary for capacitation of the spermatozoa and early embryonic development. The aim of the present study was to determine the effects of estrous cycle phases (follicular and luteal) on some biological parameters (enzymes, electrolytes and total proteins) in uterine and oviducal secretions of ewes. Oviducal and uterine fluids were collected, diluted and centrifuged. According to our results, concentrations of GPT, G6PDH, total proteins, K and Na were significantly (P <0.05) higher at the luteal phase, however, the levels of aldolase, Mg, Ca and P were significantly (P <0.05) higher at the follicular phase in uterine secretions. While, only oviducal K and Ca were significantly (P<0.05) higher at the follicular phase. Our study revealed the existence of significant cyclic variations for some uterine and oviducal parameters which indicates the effect of ovarian hormones on the components of genital secretions.

Keywords: Biochemical parameters, estrous cycle, ewe, genital secretion.

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

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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: Magda S. Taipina, Maria L. Garbelotti, Mariana G.B. Cadioli

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Banana is one of the most consumed fruits in the tropics and subtropics. Brazil accounts for about 9% of the world banana production. However, the production losses are as high as 30 to 40% and even much higher in some developing countries. The green banana flour is a complex carbohydrate source, including a high total starch (73.4%), resistant starch (17.5%) with functional properties. Gamma irradiation is considered to be an alternative method for food preservation. It has been performed due to the need of extending the shelf - life of foods, whilst maintaining their safety and avoiding one of the main concerns: the nutrient loss. In this work data about on the effects of ionizing radiation on the physicochemical analysis (carbohydrate, proteins, lipids, alimentary fiber, moistures and ashes) of Brazilian functional products (biscuits and bread) of the green banana pulp are presented. The caloric value was calculated. No significant difference was observed between the samples of irradiated and non – irradiated green banana biscuits with the following determinations: carbohydrates, proteins, alimentary fiber and ashes. Only a small significant difference was found in lipids (macronutrients). The results of physical chemical analysis of the irradiated and non- irradiated green banana bread non- irradiated showed no significant difference with the following determinations: carbohydrates, lipids (macronutrients), moisture, ashes and caloric value. A small difference was found in proteins (macronutrients). Irradiation of functional products (biscuits and bread) with doses of 1 and 3kGy maintained their original macronutrients content, showing good radioresistance.

Keywords: Irradiation, Functional Food, Nutritional value.

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Authors: Razvan Bocu, Dr Sabin Tabirca

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The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents the latest authors- achievements regarding the analysis of the networks of proteins (interactome networks), by computing more efficiently the betweenness centrality measure. The paper introduces the concept of betweenness centrality, and then describes how betweenness computation can help the interactome net- work analysis. Current sequential implementations for the between- ness computation do not perform satisfactory in terms of execution times. The paper-s main contribution is centered towards introducing a speedup technique for the betweenness computation, based on modified shortest path algorithms for sparse graphs. Three optimized generic algorithms for betweenness computation are described and implemented, and their performance tested against real biological data, which is part of the IntAct dataset.

Keywords: Betweenness centrality, interactome networks, protein-protein interactions, sub-communities, sparse networks, speedup tech-nique, IntAct.

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Authors: Ming-Lun Chiang, Hsi-Chia Chen, Chieh Wu, Yu-Ting Tseng, Ming-Ju Chen

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In this study, three strains of Vibrio parahaemolyticus (690, BCRC 13023 and BCRC 13025) were subjected to acid adaptation at pH 5.5 for 90 min. The survival of acid-adapted and non-adapted V. parahaemolyticus strains under simulated gastric condition and their protein expression profiles were investigated. Results showed that acid adaptation increased the survival of the test V. parahaemolyticus strains after exposure to simulated gastric juice (pH 3). Additionally, acid adaptation also affected the protein expression in these V. parahaemolyticus strains. Nine proteins, identified as atpA, atpB, DnaK, GroEL, OmpU, enolase, fructose-bisphosphate aldolase, phosphoglycerate kinase and triosephosphate isomerase, were induced by acid adaptation in two or three of the test strains. These acid-adaptive proteins may play important regulatory roles in the acid tolerance response (ATR) of V. parahaemolyticus.

Keywords: Acid adaptation, protein expression, simulated gastric juice, Vibrio parahaemolyticus

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Authors: Ivan Živanović, Žužana Vaštag, Senka Popović, Ljiljana Popović, Draginja Peričin

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The present work represents an investigation of the hydrolysis of hull-less pumpkin (Cucurbita Pepo L.) oil cake protein isolate (PuOC PI) by pepsin. To examine the effectiveness and suitability of pepsin towards PuOC PI the kinetic parameters for pepsin on PuOC PI were determined and then, the hydrolysis process was studied using Response Surface Methodology (RSM). The hydrolysis was carried out at temperature of 30°C and pH 3.00. Time and initial enzyme/substrate ratio (E/S) at three levels were selected as the independent parameters. The degree of hydrolysis, DH, was mesuared after 20, 30 and 40 minutes, at initial E/S of 0.7, 1 and 1.3 mA/mg proteins. Since the proposed second-order polynomial model showed good fit with the experimental data (R2 = 0.9822), the obtained mathematical model could be used for monitoring the hydrolysis of PuOC PI by pepsin, under studied experimental conditions, varying the time and initial E/S. To achieve the highest value of DH (39.13 %), the obtained optimum conditions for time and initial E/S were 30 min and 1.024 mA/mg proteins.

Keywords: Enzymatic hydrolysis, Pepsin, Pumpkin (CucurbitaPepo L.) oil cake protein isolate, Response surface methodology.

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Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

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Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility including albumin, globulin, glutenin and prolamin or gliadin. Gliadins are major components of the storage proteins in wheat endosperm. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, in terms of coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected for this study. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 93% of the accessions carried allele 210 bp, and only 8% did not any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: Diploied wheat, gliadin, Triticum boeoticum, Triticum urartu.

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Authors: Yan Ren, Fei Guo, Jun Qiao, Shengwei Hu, Hui Zhang, Yuanzhi Wang, Pengyan Wang, Jinliang Sheng, Xinli Gu, Xiaojun Liu, Chuangfu Chen

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Bovine viral diarrhea virus (BVDV) can cause lifelong persistent infection. One reason for the phenomena is attributed to BVDV infection to placenta tissue. However the mechanisms that BVDV invades into placenta tissue remain unclear. To clarify the molecular mechanisms, we investigated the possible means that BVDV entered into bovine trophoblast cells (TPC). Yeast two-hybrid system was used to identify proteins extracted from TPC, which interact with BVDV envelope glycoprotein E2. A PGbkt7-E2 yeast expression vector and TPC cDNA library were constructed. Through two rounds of screening, three positive clones were identified. Sequencing analysis indicated that all the three positive clones encoded the same protein clathrin. Physical interaction between clathrin and BVDV E2 protein was further confirmed by coimmunoprecipitation experiments. This result suggested that the clathrin might play a critical role in the process of BVDV entry into placenta tissue and might be a novel antiviral target for preventing BVDV infection.

Keywords: Bovine viral diarrhea virus, clathrin, glycoprotein E2, yeast two-hybrid system.

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Authors: Ilze Beitane

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The influence of flakes from biologically activated hull-less barley grain and malt extract on chemical composition of yoghurt was studied. Pasteurized milk, freeze-dried yoghurt culture YF-L811 (Chr. Hansen, Denmark), flakes from biologically activated hull-less barley grain (Latvia) and malt extract (Ilgezeem, Latvia) were used for experiments. Yoghurt samples with and without flakes from biologically activated hull-less barley grain and malt extract were analyzed for content of total solids, total proteins, fats, amino acids and riboflavin. The addition of flakes from biologically activated hull-less barley grain and malt extract allowed increase of nutritional value of yoghurt samples. There was obtained the increase of total proteins (p>0.05) and the decrease of fat (p>0.05). The presence of flakes from biologically activated hull-less barley grain and malt extract in yoghurt samples provided significant increase of amino acids amount (p<0.05) and riboflavin concentration (p<0.05).

Keywords: Chemical composition, hull-less barley grain, malt extract, yoghurt.

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

Abstract:

Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase–pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed-specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: Kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization.

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

Abstract:

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: L. K. Davis

Abstract:

The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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