Scholarly

Quantitative Characteristics of Rainbow Trout, Oncorhynchus Mykiss, Neo-Males (XX Genotype) and Super-Males (YY Genotype) Sperm

Year: 2011 Volume: 5 Issue: 5 277 - 284 Pages

Abstract: Rainbow trout homogametic males, (XX or YY sex genotype), can be obtained, respectively, through masculinisation of genetic females or induced androgenesis. Aim of this study was to compare reproductive potential of neo-males (XX) and super-males (YY) with heterogametic males (XY). We measured spermatozoa motility parameters, sperm concentration, osmolality and characterized protein profiles in samples of stripped and testicular sperm obtained from XY and YY males, and testicular sperm of XX males. The motile spermatozoa, as measured by both subjective method and CASA, showed no differences between testicular sperm of XX males and stripped sperm of XY and YY males whereas testicular sperm of XY and YY males had significantly lower sperm motility. Result of protein densitometry showed similarities in protein profile between seminal plasma of XY and YY males and testicular fluids of XX males. Testis of XX males showed specific histological structures of cysts consists hypertrophied Sertoli cells.

Continuous Flow Experimental Set-Up for Fouling Deposit Study

Year: 2010 Volume: 4 Issue: 8 607 - 610 Pages

Abstract: The study of the fouling deposition of pink guava juice (PGJ) is relatively new research compared to milk fouling deposit. In this work, a new experimental set-up was developed to imitate the fouling formation in heat exchanger, namely a continuous flow experimental set-up heat exchanger. The new experimental setup was operated under industrial pasteurization temperature of PGJ, which was at 93°C. While the flow rate and pasteurization period were based on the experimental capacity, which were 0.5 and 1 liter/min for the flow rate and the pasteurization period was set for 1 hour. Characterization of the fouling deposit was determined by using various methods. Microstructure of the deposits was carried out using ESEM. Proximate analyses were performed to determine the composition of moisture, fat, protein, fiber, ash and carbohydrate content. A study on the hardness and stickiness of the fouling deposit was done using a texture analyzer. The presence of seedstone in pink guava juice was also analyzed using a particle analyzer. The findings shown that seedstone from pink guava juice ranging from 168 to 200μm and carbohydrate was found to be a major composition (47.7% of fouling deposit consists of carbohydrate). Comparison between the hardness and stickiness of the deposits at two different flow rates showed that fouling deposits were harder and denser at higher flow rate. Findings from this work provide basis knowledge for further study on fouling and cleaning of PGJ.

A Probability based Pair Extension Method in Protein 2-DE Gel Image Analysis

Year: 2007 Volume: 1 Issue: 8 2519 - 2525 Pages

Abstract: The two-dimensional gel electrophoresis method (2-DE) is widely used in Proteomics to separate thousands of proteins in a sample. By comparing the protein expression levels of proteins in a normal sample with those in a diseased one, it is possible to identify a meaningful set of marker proteins for the targeted disease. The major shortcomings of this approach involve inherent noises and irregular geometric distortions of spots observed in 2-DE images. Various experimental conditions can be the major causes of these problems. In the protein analysis of samples, these problems eventually lead to incorrect conclusions. In order to minimize the influence of these problems, this paper proposes a partition based pair extension method that performs spot-matching on a set of gel images multiple times and segregates more reliable mapping results which can improve the accuracy of gel image analysis. The improved accuracy of the proposed method is analyzed through various experiments on real 2-DE images of human liver tissues.

SeqWord Gene Island Sniffer: a Program to Study the Lateral Genetic Exchange among Bacteria

Year: 2009 Volume: 3 Issue: 10 2411 - 2416 Pages

Abstract: SeqWord Gene Island Sniffer, a new program for the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial genomes and further analyzed by sequence similarity and the functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome. php). The developed computer program and the database provide the information valuable for further investigation of the distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.

An Immunosensor for Bladder Cancer Screening

Year: 2012 Volume: 6 Issue: 6 230 - 232 Pages

Abstract: Nuclear matrix protein 22 (NMP22) is a FDA approved biomarker for bladder cancer. The objective of this study is to develop a simple NMP22 immumosensor (NMP22-IMS) for accurate measurement of NMP22. The NMP22-IMS was constructed with NMP22 antibody immobilized on screen-printed carbon electrodes. The construction procedures and antibody immobilization are simple. Results showed that the NMP22-IMS has an excellent (r2³0.95) response range (20 – 100 ng/mL). In conclusion, a simple and reliable NMP22-IMS was developed, capable of precisely determining urine NMP22 level.

Increasing Chickpea Quality and Agroecosystm Sustainability Using Organic and Natural Resources

Year: 2009 Volume: 3 Issue: 9 470 - 477 Pages

Abstract: In order to increase in chickpea quality and agroecosystem sustainability, field experiments were carried out in 2007 and 2008 growing seasons. In this research the effects of different organic, chemical and biological fertilizers were investigated on grain yield and quality of chickpea. Experimental units were arranged in split-split plots based on randomized complete blocks with three replications. The highest amounts of yield and yield components were obtained in G1×N5 interaction. Significant increasing of N, P, K, Fe and Mg content in leaves and grains emphasized on superiority of mentioned treatment because each one of these nutrients has an approved role in chlorophyll synthesis and photosynthesis ability of the crop. The combined application of compost, farmyard manure and chemical phosphorus (N5) had the best grain quality due to high protein, starch and total sugar contents, low crude fiber and reduced cooking time.

Protein-Protein Interaction Detection Based on Substring Sensitivity Measure

Year: 2007 Volume: 1 Issue: 1 9 - 15 Pages

Abstract: Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Optimization of Protein Hydrolysate Production Process from Jatropha curcas Cake

Year: 2009 Volume: 3 Issue: 5 250 - 253 Pages

Abstract: This was the first document revealing the investigation of protein hydrolysate production optimization from J. curcas cake. Proximate analysis of raw material showed 18.98% protein, 5.31% ash, 8.52% moisture and 12.18% lipid. The appropriate protein hydrolysate production process began with grinding the J. curcas cake into small pieces. Then it was suspended in 2.5% sodium hydroxide solution with ratio between solution/ J. curcas cake at 80:1 (v/w). The hydrolysis reaction was controlled at temperature 50 °C in water bath for 45 minutes. After that, the supernatant (protein hydrolysate) was separated using centrifuge at 8000g for 30 minutes. The maximum yield of resulting protein hydrolysate was 73.27 % with 7.34% moisture, 71.69% total protein, 7.12% lipid, 2.49% ash. The product was also capable of well dissolving in water.

Proteolytic Dedradation of Anchovy (Spolephorus spp.) Proteins by Halophilic Proteinase from Halobacillus sp. SR5-3

Year: 2012 Volume: 6 Issue: 8 603 - 607 Pages

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

Revea Ling Casein Micelle Dispersion under Various Ranges of Nacl: Evolution of Particles Size and Structure

Year: 2011 Volume: 5 Issue: 1 21 - 25 Pages

Abstract: Dispersions of casein micelles (CM) were studied at a constant protein concentration of 5 wt % in high NaCl environment ranging from 0% to 12% by Dynamic light scattering (DLS) and Fourier Transform Infrared (FTIR). The rehydration profiles obtained were interpreted in term of wetting, swelling and dispersion stages by using a turbidity method. Two behaviours were observed depending on the salt concentration. The first behaviour (low salt concentration) presents a typical rehydration profile with a significant change between 3 and 6% NaCl indicating quick wetting, swelling and long dispersion stage. On the opposite, the dispersion stage of the second behaviour (high salt concentration) was significantly shortened indicating a strong modification of the protein backbone. A salt increase result to a destabilization of the micelle and the formation of mini-micelles more or less aggregated indicating an average micelles size ranging from 100 to 200 nm. For the first time, the estimations of secondary structural elements (irregular, ß-sheet, α-helix and turn) by the Amide III assignments were correlated with results from Amide I.

High Glucose Increases Acetylcholine-Induced Ca2+ Entry and Protein Expression of STIM1

Year: 2012 Volume: 6 Issue: 4 87 - 90 Pages

Abstract: Hyperglycaemia is a key factor that contributes to the development of diabetes-related microvascular disease and a major risk factor for endothelial dysfunction. In the current study, we have explored glucose-induced abnormal intracellular calcium (Ca2+ i) homeostasis in mouse microvessel endothelial cells (MMECs) in high glucose (HG) (40mmol/L) versus control (low glucose, LG) (11 mmol/L). We demonstrated that the exposure of MMECs to HG for 3 days did not change basal Ca2+ i, however, there was a significant increase of acetylcholine-induced Ca2+ entry. Western blots illustrated that exposure to HG also increased STIM1 (Stromal Interaction Molecule 1), but not Orai1 (the pore forming subunit), protein expression levels. Although the link between HG-induced changes in STIM1 expression, enhanced Ca2+ entry and endothelial dysfunction requires further study, the current data are suggestive that targeting these pathways may reduce the impact of HG on endothelial function.

PmSPARQL: Extended SPARQL for Multi-paradigm Path Extraction

Year: 2008 Volume: 2 Issue: 2 446 - 457 Pages

Abstract: In the last few years, the Semantic Web gained scientific acceptance as a means of relationships identification in knowledge base, widely known by semantic association. Query about complex relationships between entities is a strong requirement for many applications in analytical domains. In bioinformatics for example, it is critical to extract exchanges between proteins. Currently, the widely known result of such queries is to provide paths between connected entities from data graph. However, they do not always give good results while facing the user need by the best association or a set of limited best association, because they only consider all existing paths but ignore the path evaluation. In this paper, we present an approach for supporting association discovery queries. Our proposal includes (i) a query language PmSPRQL which provides a multiparadigm query expressions for association extraction and (ii) some quantification measures making easy the process of association ranking. The originality of our proposal is demonstrated by a performance evaluation of our approach on real world datasets.

An Information Theoretic Approach to Rescoring Peptides Produced by De Novo Peptide Sequencing

Year: 2010 Volume: 4 Issue: 10 728 - 733 Pages

Abstract: 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.

Sericin Film: Influence of Concentration on its Physical Properties

Year: 2009 Volume: 3 Issue: 8 209 - 211 Pages

Abstract: 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.

Using Spectral Vectors and M-Tree for Graph Clustering and Searching in Graph Databases of Protein Structures

Year: 2009 Volume: 3 Issue: 8 2027 - 2032 Pages

Abstract: 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.

Determination of Yield and Some Quality Characteristics of Winter Canola (Brassica napus ssp. oleifera L.) Cultivars

Year: 2014 Volume: 8 Issue: 9 983 - 989 Pages

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.

Smart Motion

Year: 2012 Volume: 6 Issue: 11 1009 - 1013 Pages

Abstract: Austenite and Martensite indicate the phases of solids undergoing phase transformation which we usually associate with materials and not with living organisms. This article provides an overview of bacterial proteins and structures that are undergoing phase transformation and suggests its probable effect on mechanical behavior. The context is mainly within the role of phase transformations occurring in the flagellum of bacteria. The current knowledge of molecular mechanism leading to phase variation in living organisms is reviewed. Since in bacteria, each flagellum is driven by a separate motor, similarity to a Differential drive in case of four-wheeled vehicles is suggested. It also suggests the application of the mechanism in which bacteria changes its direction of movement to facilitate single point turning of a multi-wheeled vehicle. Finally, examples are presented to illustrate that the motion due to phase transformation of flagella in bacteria can start a whole new research on motion mechanisms.

Optimization of Enzymatic Activities in Malting of Oat

Year: 2010 Volume: 4 Issue: 7 463 - 468 Pages

Abstract: Malting is usually carried out on intact barley seed, while hull is still attached to it. In this study, oat grain with and without hull was subjected to controlled germination to optimize its enzymes activity, in such a way that lipase has the lowest and α- amylase and proteinase the highest activities. Since pH has a great impact on the activity of the enzymes, the pH of germination media was set up to 3 to 8. In dehulled oats, lipase and α-amylase had the lowest and highest activities in pHs 3 and 6, respectively whereas the highest proteinase activity was evidenced at pH 7 and 4 in the oats with and without hull respectively. While measurements indicated that the effect of hull on the enzyme activities particularly in lipase and amylase at each level of the pH are significantly different, the best results were obtained in those samples in which their hull had been removed. However, since the similar lipase activity in germinated dehulled oat were recorded at the pHs 4 and 5, therefore it was concluded that pH 5 in dehulled oat seed may provide the optimum enzyme activity for all the enzymes.

Are PEG Molecules a Universal Protein Repellent?

Year: 2009 Volume: 3 Issue: 1 41 - 45 Pages

Abstract: 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.

A Novel Approach for Protein Classification Using Fourier Transform

Year: 2010 Volume: 4 Issue: 8 594 - 598 Pages

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.

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