Search results for: rice bran protein.

Authors: Maria E. Manioudaki, Panayiota Poirazi

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Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.

Keywords: gene modules, artificial neural networks, yeast, stress

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Authors: V. K. Krishnan, T. Balusamy

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A solar dish collector has been designed, fabricated and tested for its performance on 10-03-2015 in Salem, Tamilnadu, India. The experiments on cooking vessels of coated and un-coated with 5 Liters capacity have been used for cooking Rice. The results are shown in graphs. The solar cooker is always capable of cooking food within the expected length of time and based on the solar radiation levels. With minimum cooking power, the coated pressure cooker of 5 Liters capacity cooks the food at faster manner. This is due to the conductivity of the coating material provided in the cooker.

Keywords: Solar cooker, solar concentrator type, thermal performance, simulation.

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

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

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

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Authors: Permphan Dharmasaroja

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Mutations of the telomeric copy of the survival motor neuron 1 (SMN1) gene cause spinal muscular atrophy. A deletion of the Eef1a2 gene leads to lower motor neuron degeneration in wasted mice. Indirect evidences have been shown that the eEF1A protein family may interact with SMN, and our previous study showed that abnormalities of neuromuscular junctions in wasted mice were similar to those of Smn mutant mice. To determine potential colocalization between SMN and tissue-specific translation elongation factor 1A2 (eEF1A2), an immunochemical analysis of HeLa cells transfected with the plasmid pcDNA3.1(+)C-hEEF1A2- myc and a new quantitative test of colocalization by intensity correlation analysis (ICA) was used to explore the association of SMN and eEF1A2. Here the results showed that eEF1A2 redistributed from the cytoplasm to the nucleus in response to serum and epidermal growth factor. In the cytoplasm, compelling evidence showed that staining for myc-tagged eEF1A2 varied in synchrony with that for SMN, consistent with the formation of a SMN-eEF1A2 complex in the cytoplasm of HeLa cells. These findings suggest that eEF1A2 may colocalize with SMN in the cytoplasm and may be a component of the SMN complex. However, the limitation of the ICA method is an inability to resolve colocalization in components of small organelles such as the nucleus.

Keywords: Intensity correlation analysis, intensity correlation quotient.

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Authors: Mardiana Ahamad Zabidi, Akmalluddin Md. Yunus

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Soursop (Anona muricata) is one of the underutilized tropical fruits containing nutrients, particularly dietary fibre and antioxidant properties that are beneficial to human health. This objective of this study is to investigate the feasibility of matured soursop pulp flour (SPF) to be substituted with high-protein wheat flour in bread. Bread formulation was substituted with different levels of SPF (0%, 5%, 10% and 15%). The effect on physicochemical properties and sensory attributes were evaluated. Higher substitution level of SPF resulted in significantly higher (p<0.05) fibre, protein and ash content, while fat and carbohydrate content reduced significantly (p<0.05). FESEM showed that the bread crumb surface of control and 5% SPF appeared to distribute evenly and coalesced by thin gluten film. However, higher SPF substitution level in bread formulation exhibited a deleterious effect by formation of discontinuous gluten network. For texture profile analysis, 5% SPF bread resulted in the lowest value of hardness. The score of sensory evaluation showed that 5% SPF bread received good acceptability and is comparable with control bread.

Keywords: Bread, Physicochemical properties, Scanning electron microscopy (SEM), Sensory attributes, Soursop pulp flour.

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Authors: L. K. Davis

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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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Authors: Simona Dostalova, Ana Maria Jimenez Jimenez, Marketa Vaculovicova, Vojtech Adam, Rene Kizek

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Various nanomaterials can be used as a drug delivery vehicles in nanomedicine, called nanocarriers. They can either be organic or inorganic, synthetic or natural-based. Although synthetic nanocarriers are easier to produce, they can often be toxic for the organism and thus not suitable for use in treatment. From naturalbased nanocarriers, the most commonly used are protein cages or viral capsids. In this work, virus bacteriophage λ was used for delivery of different cytotoxic drugs (cisplatin, carboplatin, oxaliplatin and doxorubicin). Large quantities of phage λ were obtained from phage λ-producing strain of E. coli cultivated in medium with 0.2% maltose. After killing of E. coli with chloroform and its removal by centrifugation, the phage was concentrated by ultracentrifugation at 130 000×g and 4°C for 3 h. The encapsulation of the drugs was performed by infusion method and four different concentrations of the drugs were encapsulated (200; 100; 50; 25 μg·mL-1). Free drug molecules were removed by filtration. The encapsulation was verified using the absorbance for doxorubicin and atomic absorption spectrometry for platinum cytostatics. The amount of encapsulated drug linearly increased with the increasing concentration of applied drug with the determination coefficient R2=0.989 for doxorubicin; R2=0.967 for cisplatin; R2=0.989 for carboplatin and R2=0.996 for oxaliplatin. The overall encapsulation efficiency was calculated as 50% for doxorubicin; 8% for cisplatin; 6% for carboplatin and 10% for oxaliplatin.

Keywords: Bacteriophage λ, doxorubicin, platinum cytostatics, protein-based nanocarrier, viral capsid.

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Authors: Vandana Bali, Manab B. Bera, Parmjit S. Panesar

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Microbial production of antimicrobials as biopreservatives is the major area of focus nowadays due to increased interest of consumers towards natural and safe preservation of ready to eat food products. The agro-industrial byproduct based medium and optimized process conditions can contribute in economical production of bacteriocins. Keeping this in view, the present investigation was carried out on agro-industrial byproducts utilization for the production of bacteriocin using Enterococcus faecium BS13 isolated from local fermented food. Different agro-industrial byproduct based carbon sources (whey, potato starch liquor, kinnow peel, deoiledrice bran and molasses), nitrogen sources (soya okra, pea pod and corn steep liquor), metal ions and surfactants were tested for optimal bacteriocin production. The effect of various process parameters such as pH, temperature, inoculum level, agitation and time were also tested on bacteriocin production. The optimized medium containing whey, supplemented with 4%corn steep liquor and polysorbate-80 displayed maximum bacteriocin activity with 2% inoculum, at pH 6.5, temperature 40^oC under shaking conditions (100 rpm).

Keywords: Bacteriocin, biopreservation, corn steep liquor, Enterococcus faecium, waste utilization, whey.

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

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

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

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Authors: F. A. M. Safwan, H. N. N. Dilrukshi, P. U. S. Peiris

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Less availability of high quality green forages leads to low productivity of national dairy herd of Sri Lanka. Growing grass and fodder to suit the production system is an efficient and economical solution for this problem. CO-3 is placed in a higher category, especially on tillering capacity, green forage yield, regeneration capacity, leaf to stem ratio, high crude protein content, resistance to pests and diseases and free from adverse factors along with other fodder varieties grown within the country. An experiment was designed to determine the effect of organic sheep manure, inorganic fertilizers and liquid sheep manure on growth, yield and nutritive value of CO-3. The study was consisted with three treatments; sheep manure (T1), recommended inorganic fertilizers (T2) and liquid sheep manure (T3) which was prepared using bucket fermentation method and each treatment was consisted with three replicates and those were assigned randomly. First harvest was obtained after 40 days of plant establishment and number of leaves (NL), leaf area (LA), tillering capacity (TC), fresh weight (FW) and dry weight (DW) were recorded and second harvest was obtained after 30 days of first harvest and same set of data were recorded. SPSS 16 software was used for data analysis. For proximate analysis AOAC, 2000 standard methods were used. Results revealed that the plants treated with T1 recorded highest NL, LA, TC, FW and DW and were statistically significant at first and second harvest of CO-3 (p˂ 0.05) and it was found that T1 was statistically significant from T2 and T3. Although T3 was recorded higher than the T2 in almost all growth parameters; it was not statistically significant (p ˃0.05). In addition, the crude protein content was recorded highest in T1 with the value of 18.33±1.61 and was lowest in T2 with the value of 10.82±1.14 and was statistically significant (p˂ 0.05). Apart from this, other proximate composition crude fiber, crude fat, ash, moisture content and dry matter were not statistically significant between treatments (p ˃0.05). In accordance with the results, it was found that the organic fertilizer is the best fertilizer for CO-3 in terms of growth parameters and crude protein content.

Keywords: Fertilizer, growth parameters, Hybrid Napier CO-3, proximate composition.

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Authors: Payel Ghosh, Rama Chandra Pradhan, Sabyasachi Mishra

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

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

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Authors: Raquel P. F. Guiné, Marlene I. C. Tenreiro, Ana C. Correia, Paulo Barracosa, Paula M. R. Correia

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The objective of this study was to evaluate the physical and chemical characteristics of Serra da Estrela cheese and compare these results with those of the sensory analysis. For the study were taken six samples of Serra da Estrela cheese produced with 6 different ecotypes of thistle in a dairy situated in Penalva do Castelo. The chemical properties evaluated were moisture content, protein, fat, ash, chloride and pH; the physical properties studied were color and texture; and finally a sensory evaluation was undertaken. The results showed moisture varying in the range 40- 48%, protein in the range 15-20%, fat between 41-45%, ash between 3.9-5.0% and chlorides varying from 1.2 to 3.0%. The pH varied from 4.8 to 5.4. The textural properties revealed that the crust hardness is relatively low (maximum 7.3 N), although greater than flesh firmness (maximum 1.7 N), and also that these cheeses are in fact soft paste type, with measurable stickiness and intense adhesiveness. The color analysis showed that the crust is relatively light (L* over 50), and with a predominant yellow coloration (b* around 20 or over) although with a slight greenish tone (a* negative). The results of the sensory analysis did not show great variability for most of the attributes measured, although some differences were found in attributes such as crust thickness, crust uniformity, and creamy flesh.

Keywords: Chemical composition, color, sensorial analysis, Serra da Estrela cheese, texture.

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Authors: A. Sharma, R. Tewari, S. K. Soni

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Biofuels production has come forth as a future technology to combat the problem of depleting fossil fuels. Bio-based ethanol production from enzymatic lignocellulosic biomass degradation serves an efficient method and catching the eye of scientific community. High cost of the enzyme is the major obstacle in preventing the commercialization of this process. Thus main objective of the present study was to optimize composition of medium components for enhancing cellulase production by newly isolated strain of Bacillus tequilensis. Nineteen factors were taken into account using statistical Plackett-Burman Design. The significant variables influencing the cellulose production were further employed in statistical Response Surface Methodology using Central Composite Design for maximizing cellulase production. The optimum medium composition for cellulase production was: peptone (4.94 g/L), ammonium chloride (4.99 g/L), yeast extract (2.00 g/L), Tween-20 (0.53 g/L), calcium chloride (0.20 g/L) and cobalt chloride (0.60 g/L) with pH 7, agitation speed 150 rpm and 72 h incubation at 37oC. Analysis of variance (ANOVA) revealed high coefficient of determination (R2) of 0.99. Maximum cellulase productivity of 11.5 IU/ml was observed against the model predicted value of 13 IU/ml. This was found to be optimally active at 60oC and pH 5.5.

Keywords: Bacillus tequilensis, CMCase, Submerged Fermentation, Optimization, Plackett-Burman Design, Response Surface Methodology.

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Authors: Vita Sterna, Sanita Zute, Inga Jansone, Linda Brunava, Inara Kantane

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Grains, including oats (Avena sativa L.), have been recognized functional foods, because provide beneficial effect on the health of the consumer and decrease the risk of various diseases. Oats are good source of soluble fibre, essential amino acids, unsaturated fatty acids, vitamins and minerals. Oat breeders have developed oat varieties and improved yielding ability potential of oat varieties. Therefore, the aim of investigation was to analyze the composition of perspective oat varieties and breeding lines grains grown in different conditions and evaluate functional properties. In the studied samples content of protein, starch, β-glucans, total dietetic fibre, composition of amino acids and vitamin E were determined. The results of analysis showed that protein content depending of varieties ranged 9.70% to 17.30% total dietary fibre 13.66 g100g-1 to 30.17 g100g-1, content of β-glucans 2.7 g100g-1 to 3.5 g100g-1, amount of vitamin E (α-tocopherol) determined from 4 mgkg-1 to 9.9 mgkg-1. The sums of essential amino acids in oat grain samples were determined from 31.63 gkg-1 to 54.90 gkg-1. It is concluded that amino acids composition of husked and naked oats grown in organic or conventional conditions is close to optimal for human health.

Keywords: Amino acids, β-glucans, dietetic fibre, nutrition value.

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Authors: Marthese Azzopardi, Liberato Camilleri

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This research was performed to investigate the study habits and level of difficulty perceived by post-secondary students in Biology at Advanced-level topics after completing their first year of study. At the end of a two-year ‘sixth form’ course, Maltese students sit for the Matriculation and Secondary Education Certificate (MATSEC) Advanced-level biology exam as a requirement to pursue science-related studies at the University of Malta. The sample was composed of 23 students (16 taking Chemistry and seven taking some ‘Other’ subject at the Advanced Level). The cohort comprised seven males and 16 females. A questionnaire constructed by the authors, was answered anonymously during the last lecture at the end of the first year of study, in May 2016. The Chi square test revealed that gender plays no effect on the various study habits (c² (6) = 5.873, p = 0.438). ‘Reading both notes and textbooks’ was the most common method adopted by males (71.4%), whereas ‘Writing notes on each topic’ was that mostly used by females (81.3%). The Mann-Whitney U test showed no significant difference in the study habits of students and the mean assessment mark obtained at the end of the first year course (p = 0.231). Statistical difference was found with the One-ANOVA test when comparing the mean assessment mark obtained at the end of the first year course when students are clustered by their Secondary Education Certificate (SEC) grade (p < 0.001). Those obtaining a SEC grade of 2 and 3 got the highest mean assessment of 68.33% and 66.9%, respectively [SEC grading is 1-7, where 1 is the highest]. The Friedman test was used to compare the mean difficulty rating scores provided for the difficulty of each topic. The mean difficulty rating score ranges from 1 to 4, where the larger the mean rating score, the higher the difficulty. When considering the whole group of students, nine topics out of 21 were perceived as significantly more difficult than the other topics. Protein synthesis, DNA Replication and Biomolecules were the most difficult, in that order. The Mann-Whitney U test revealed that the perceived level of difficulty in comprehending Biomolecules is significantly lower for students taking Chemistry compared to those not choosing the subject (p = 0.018). Protein Synthesis was claimed as the most difficult by Chemistry students and Biomolecules by those not studying Chemistry. DNA Replication was the second most difficult topic perceived by both groups. The Mann-Whitney U test was used to examine the effect of gender on the perceived level of difficulty in comprehending various topics. It was found that females have significantly more difficulty in comprehending Biomolecules than males (p=0.039). Protein synthesis was perceived as the most difficult topic by males (mean difficulty rating score = 3.14), while Biomolecules, DNA Replication and Protein synthesis were of equal difficulty for females (mean difficulty rating score = 3.00). Males and females perceived DNA Replication as equally difficult (mean difficulty rating score = 3.00). Discovering the students’ study habits and perceived level of difficulty of specific topics is vital for the lecturer to offer guidance that leads to higher academic achievement.

Keywords: Biology, Perceived difficulty, Post-secondary, Study habits.

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

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The aim of this study was to estimate the frequency of EBV infection in Hodgkin's lymphoma (HL) and non-Hodgkin's lymphoma (NHL) occurring in Jordanian patients. A total of 55 patients with lymphoma were examined in this study. Of 55 patients, 30 and 25 were diagnosed as HL and NHL, respectively. The four HL subtypes were observed with the majority of the cases exhibited the mixed cellularity (MC) subtype followed by the nodular sclerosis (NS). The high grade was found to be the commonest subtype of NHL in our sample, followed by the low grade. The presence of EBV virus was detected by immunostating for expression of latent membrane protein-1 (LMP-1). The frequency of LMP-1 expression occurred more frequent in patients with HL (60.0%) than in patients with NHL (32.0%). The frequency of LMP-1 expression was also higher in patients with MC subtype (61.11%) than those patients with NS (28.57%). No age or gender difference in occurrence of EBV infection was observed among patient with HL. By contrast, the prevalence of EBV infection in NHL patients aged below 50 was lower (16.66%) than in NHL patients aged 50 or above (46.15%). In addition, EBV infection was more frequent in females with NHL (38.46%) than in male with NHL (25%). In NHL cases, the frequency of EBV infection in intermediate grade (60.0%) was high when compared with frequency of low (25%) or high grades (25%). In conclusion, analysis of LMP-1 expression indicates an important role for this viral oncogene in the pathogenesis of EBV-associated malignant lymphomas. These data also support the previous findings that people with EBV may develop lymphoma and that efforts to maintain low lymphoma should be considered for people with EBV infection.

Keywords: Hodgkin lymphoma, Epstein Barr virus, hematoxylin, infection, LMP-1 expression.

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Authors: Vikas Tewari, Shivendra Tewari, K. R. Pardasani

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Calcium is a vital second messenger used in signal transduction. Calcium controls secretion, cell movement, muscular contraction, cell differentiation, ciliary beating and so on. Two theories have been used to simplify the system of reaction-diffusion equations of calcium into a single equation. One is excess buffer approximation (EBA) which assumes that mobile buffer is present in excess and cannot be saturated. The other is rapid buffer approximation (RBA), which assumes that calcium binding to buffer is rapid compared to calcium diffusion rate. In the present work, attempt has been made to develop a model for calcium diffusion under excess buffer approximation in neuron cells. This model incorporates the effect of [Na+] influx on [Ca2+] diffusion,variable calcium and sodium sources, sodium-calcium exchange protein, Sarcolemmal Calcium ATPase pump, sodium and calcium channels. The proposed mathematical model leads to a system of partial differential equations which have been solved numerically using Forward Time Centered Space (FTCS) approach. The numerical results have been used to study the relationships among different types of parameters such as buffer concentration, association rate, calcium permeability.

Keywords: Excess buffer approximation, Na+ influx, sodium calcium exchange protein, sarcolemmal calcium atpase pump, forward time centred space.

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Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

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Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

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Authors: Chang Kug Kim, Dong Suk Park, Young Joo Seol, Jang Ho Hahn

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The National Agricultural Biotechnology Information Center (NABIC) plays a leading role in the biotechnology information database for agricultural plants in Korea. Since 2002, we have concentrated on functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on bioinformatics of major agricultural resources such as rice, Chinese cabbage, and microorganisms. In the NABIC, integration-based biotechnology database provides useful information through a user-friendly web interface that allows analysis of genome infrastructure, multiple plants, microbial resources, and living modified organisms.

Keywords: biotechnology, database, genome information

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

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Salt stress adversely affects plant growth at various stages of development including seed germination, seedling establishment, vegetative growth and finally reproduction. Because of their immobile nature, plants have evolved mechanisms to sense and respond to salt stress. Seed dormancy is an adaptive trait that enables seed germination to coincide with favorable environmental conditions. We identified a novel locus of Arabidopsis, designated SHG1 (salt hypersensitive germination 1), whose disruption leads to reduced germination rate under moderate salt stress conditions. SHG1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. The shg1-disrupted Arabidopsis mutant died at the cotyledon stage when sown on salt-containing medium, although wild-type plants could form true leaves under the same conditions. On the other hand, this mutant showed similar phenotypes to wild-type plants when sown on medium without salt and transferred to salt-containing medium at the vegetative stage. These results suggested that SHG1 played indispensable role in the seed germination and seedling establishment under moderate salt stress conditions. SHG1 may be involved in the release of seed dormancy.

Keywords: Germination, ankyrin repeat, Arabidopsis, salt tolerance.

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Authors: C. S. Saini

Abstract:

The composite flour blend consisting of corn, pearl millet, black gram and wheat bran in the ratio of 80:5:10:5 was taken to prepare the extruded product and their effect on physical properties of extrudate was studied. The extrusion process was conducted in laboratory by using twin screw extruder. The physical characteristics evaluated include lateral expansion, bulk density, water absorption index, water solubility index, and rehydration ratio and moisture retention. The Central Composite Rotatable Design (CCRD) was used to decide the level of processing variables i.e. feed moisture content (%), screw speed (rpm), and barrel temperature (oC) for the experiment. The data obtained after extrusion process were analyzed by using response surface methodology. A second order polynomial model for the dependent variables was established to fit the experimental data. The numerical optimization studies resulted in 127°C of barrel temperature, 246 rpm of screw speed, and 14.5% of feed moisture as optimum variables to produce acceptable extruded product. The responses predicted by the software for the optimum process condition resulted in lateral expansion 126%, bulk density 0.28 g/cm3, water absorption index 4.10 g/g, water solubility index 39.90%, rehydration ratio 544% and moisture retention 11.90% with 75% desirability.

Keywords: Black gram, corn flour, extrusion, physical characteristics.

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Authors: Zafer Ceylan, Gülgün F. Unal Sengor, Onur Gönülal

Abstract:

The differences on proximate composition, sensorial analysis (for raw and cooked samples) and flesh productivity of the samples of Parapenaus longirostris that were caught in the North Aegean Sea and Marmara Sea were investigated. Moisture, protein, lipid, ash, carbohydrate, energy content of the North Aegean Sea shrimp were found 74.92 ± 0.1, 20.32 ± 0.16, 2.55 ± 0.1, 2.13 ± 0.08, 0.08%, 110.1 kcal/100 g, respectively. On the other hand, the Marmara Sea shrimp was found 76.9 ± 0.02, 19.06 ± 0.03, 2.22 ± 0.08, 1.51 ± 0.04, 0.33, 102.77 kcal/100g, respectively. Protein, lipid, ash and energy values of the Northern Aegean Sea shrimp were higher than the Marmara Sea shrimp. On the other hand, moisture, carbohydrate values of the Northern Aegean Sea shrimp were lower than the Marmara samples. Sensorial analyses were carried on for raw and cooked samples. Among all properties for raw samples, flesh color, shrimp connective tissue, shrimp body parameters were different from each other according to the result of the panel. According to the result of the cooked shrimp samples among all properties, cooked odour, flavor and texture were different from each other as well. Especially, flavor and textural properties of cooked shrimps of the Northern Aegean Sea were higher than the Marmara Sea shrimp. The flesh yield of the Northern Aegean Sea shrimp was found 46.42%, while Marmara Sea shrimp was found 47.74%.

Keywords: Proximate value, sensorial evaluation, Parapenaus longirostris flesh yield.

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Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

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

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

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Authors: Mustafa M. Donma, Orkide Donma

Abstract:

A growing list of cancers might be influenced by obesity. Obesity is associated with an increased risk for the occurrence and development of some cancers. Inflammation can lead to cancer. It is one of the characteristic features of cancer and plays a critical role in cancer development. C-reactive protein (CRP) is under evaluation related to the new and simple prognostic factors in patients with metastatic renal cell cancer. Obesity can predict and promote systemic inflammation in healthy adults. BMI is correlated with hs-CRP. In this study, SII index and CRP values were evaluated in children with normal BMI and those within the range of different obesity grades to detect the tendency towards cancer in pediatric obesity. A total of one hundred and ninety-four children; thirty-five children with normal BMI, twenty overweight (OW), forty-seven obese (OB) and ninety-two morbid obese (MO) participated in the study. Age- and sex-matched groups were constituted using BMI-for age percentiles. Informed consent was obtained. Ethical Committee approval was taken. Weight, height, waist circumference (C), hip C, head C and neck C of the children were measured. The complete blood count test was performed. C-reactive protein analysis was performed. Statistical analyses were performed using SPSS. The degree for statistical significance was p≤0.05. SII index values were progressively increasing starting from normal weight (NW) to MO children. There is a statistically significant difference between NW and OB as well as MO children. No significant difference was observed between NW and OW children, however, a correlation was observed between NW and OW children. MO constitutes the only group, which exhibited a statistically significant correlation between SII index and CRP. Obesity-related bladder, kidney, cervical, liver, colorectal, endometrial cancers are still being investigated. Obesity, characterized as a chronic low-grade inflammation, is a crucial risk factor for colon cancer. Elevated childhood BMI values may be indicative of processes leading to cancer, initiated early in life. Prevention of childhood adiposity may decrease the cancer incidence in adults. To authors’ best knowledge, this study is the first to introduce SII index values during obesity of varying degrees of severity. It is suggested that this index seems to affect all stages of obesity with an increasing tendency and may point out the concomitant status of obesity and cancer starting from very early periods of life.

Keywords: Children, c- reactive protein, systemic immune-inflammation index, obesity.

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Authors: Chan-Jung Liang, Shu-Huei Wang, Pei-Jhen Wu, Jaw-Shiun Tsai, Chau-Chung Wu, Yuh-Lien Chen

Abstract:

Heme oxygenase-1 (HO-1), an enzyme degrading heme to carbon monoxide, iron, and biliverdin, has been recognized as playing a crucial role in cellular defense against stressful conditions, not only related to heme release. In the present study, the effects of TNF-a on the expression of heme oxygenase-1 (HO-1) in human aortic endothelial cells (HAECs) as well as the related mechanisms were investigated. 10 ng/mL TNF-α treatment significantly increased HO-1 expression after 6h, then a further increase at 12h and declined at 24h. Treatment with 2 ng/mL of TNF-a after 12 h resulted in a significant increase in HO-1 expression, which peaked at 10 ng/mL, then declined at 20 ng/mL. TNF-α induced HO-1 expression and then HO-1 expression reduced  vascular cell adhesion molecule-1 (VCAM-1) expression. Phosphorylation studies of ERK1/2, JNK, and p38, three subgroups of mitogen-activated protein kinases (MAPKs) demonstrated TNF-α-induced ERK1/2, JNK, and p38 phosphorylation. The increase in HO-1 expression in response to TNF-α treatment was affected by pretreatment with SP600125 (a JNK inhibitor) and SB203580 (a p38 inhibitor), not with PD98059 (an ERK1/2 inhibitor). The expression of HO-1 was stronger in aortas of TNF-α-treated apo-E deficient mice when compared with control mice. These results suggest that low dose of TNF-α treatment notably induced HO-1 expression was mediated through JNK/p38 phosphorylation and may have a protective potential in cardiovascular diseases and inflammatory response through the regulation of HO-1 expression.

Keywords: Heme oxygenase-1 inflammation, endothelial cells, mitogen-activated protein kinases (MAPKs).

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Authors: Phuong T. Dang, Hy G. Le, Giang T. Pham, Hong T. M. Vu, Kien T, Nguyen, Canh D. Dao, Giang H. Le, Hoa T. K. Tran, Quang K. Nguyen, Tuan A. Vu

Abstract:

Nanostructured catalysts were successfully prepared by acidification of diatomite and regeneration of FCC spent catalysts. The obtained samples were characterized by IR, XRD, SEM, EDX, MAS-NMR (27Al and 29Si), NH3-TPD and tested in catalytic pyrolysis of biomass (rice straw). The results showed that the similar bio-oil yield of 41.4% can be obtained by pyrolysis with catalysts at 450oC as compared to that of the pyrolysis without catalyst at 550oC. The bio-oil yield reached a maximum of 42.55% at the pyrolysis temperature of 500oC with catalytic content of 20%. Moreover, by catalytic pyrolysis, bio-oil quality was better as reflected in higher ratio of H/C, lower ratio of O/C. This clearly indicated high application potential of these new nanostructured catalysts in the production of bio-oil with low oxygenated compounds.

Keywords: Acidified diatomite, biomass, catalytic pyrolysis, bio-oil, nanostructured catalysts, regenerated FCC catalyst.

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Authors: Pattaranut Eakwaropas, Khemjira Jarmkom, Warachate Khobjai, Surachai Techaoei

Abstract:

The aim of this study is to improve Pang-Rum (PR) hardness by adding natural binders. PR is one of Thai tradition aroma products. In the past, it was used for aesthetic propose on face and body with good odor. Nowadays, PR is not popular and going to be disappeared. Five natural materials, i.e. agar, rice flour, glutinous flour, corn starch, and tapioca starch were selected to use as binders. Binders were dissolved with boiled water into concentration 5% and 10% w/w except agar that was prepared 0.5% and 1% w/w. PR with and without binder were formulated. Physical properties, i.e. weight, shape, color, and hardness were evaluated. PR with 10% of corn starch solution had suitable hardness (14.2±0.9 kg) and the best appearance. In the future, it would be planned to study about odor and physical stability for decorated product development.

Keywords: Aromatic water, hardness, natural binder, pang-rum.

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Authors: Ayodeji Fasuyi

Abstract:

Telfairia occidentalis is a leafy vegetable commonly grown in the tropics for nutritional benefits. The use of enzymes and probiotics is becoming prominent due to the ban on antibiotics as growth promoters in many parts of the world. It is conceived that with enzymes and probiotics additives, fibrous leafy vegetables can be incorporated into poultry feeds as protein source. However, certain antinutrients were also found in the leaves of Telfairia occidentalis. Four broiler starter and finisher diets were formulated for the two phases of the broiler experiments. A mixture of fiber degrading enzymes, Roxazyme G2 (combination of cellulase, glucanase and xylanase) and probiotics (Turbotox), a growth promoter, were used in broiler diets at 1:1. The Roxazyme G2/Turbotox mixtures were used in diets containing four varying levels of Telfairia occidentalis leaf meal (TOLM) at 0, 10, 20 and 30%. Diets 1 were standard broiler diets without TOLM and Roxazyme G2 and Turbotox additives. Diets 2, 3 and 4 had enzymes and probiotics additives. Certain mineral elements such as Ca, P, K, Na, Mg, Fe, Mn, Cu and Zn were found in notable quantities viz. 2.6 g/100 g, 1.2 g/100 g, 6.2 g/100 g, 5.1 g/100 g, 4.7 g/100 g, 5875 ppm, 182 ppm, 136 ppm and 1036 ppm, respectively. Phytin, phytin-P, oxalate, tannin and HCN were also found in ample quantities viz. 189.2 mg/100 g, 120.1 mg/100 g, 80.7 mg/100 g, 43.1 mg/100 g and 61.2 mg/100 g, respectively. The average weight gain was highest at 46.3 g/bird/day for birds on 10% TOLM diet but similar (P > 0.05) to 46.2 g/bird/day for birds on 20% TOLM. The feed conversion ratio (FCR) of 2.27 was the lowest and optimum for birds on 10% TOLM although similar (P > 0.05) to 2.29 obtained for birds on 20% TOLM. FCR of 2.61 was the highest at 2.61 for birds on 30% TOLM diet. The lowest FCR of 2.27 was obtained for birds on 10% TOLM diet although similar (P > 0.05) to 2.29 for birds on 20% TOLM diet. Most carcass characteristics and organ weights were similar (P > 0.05) for the experimental birds on the different diets except for kidney, gizzard and intestinal length. The values for kidney, gizzard and intestinal length were significantly higher (P < 0.05) for birds on the TOLM diets. The nitrogen retention had the highest value of 72.37 ± 0.10% for birds on 10% TOLM diet although similar (P > 0.05) to 71.54 ± 1.89 obtained for birds on the control diet without TOLM and enzymes/probiotics mixture. There was evidence of a better utilization of TOLM as a plant protein source. The carcass characteristics and organ weights all showed evidence of uniform tissue buildup and muscles development particularly in diets containing 10% of TOLM level. There was also better nitrogen utilization in birds on the 10% TOLM diet. Considering the cheap cost of TOLM, it is envisaged that its introduction into poultry feeds as a plant protein source will ultimately reduce the cost of poultry feeds.

Keywords: Telfairia occidentalis leaf meal, enzymes, probiotics, additives.

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Authors: S. S. Rana, C. Janveja, S. K. Soni

Abstract:

This study is concerned with the optimization of fermentation parameters for the hyper production of mannanase from Fusarium oxysporum SS-25 employing two step statistical strategy and kinetic characterization of crude enzyme preparation. The Plackett-Burman design used to screen out the important factors in the culture medium revealed 20% (w/w) wheat bran, 2% (w/w) each of potato peels, soyabean meal and malt extract, 1% tryptone, 0.14% NH4SO4, 0.2% KH2PO4, 0.0002% ZnSO4, 0.0005% FeSO4, 0.01% MnSO4, 0.012% SDS, 0.03% NH4Cl, 0.1% NaNO3 in brewer’s spent grain based medium with 50% moisture content, inoculated with 2.8×107 spores and incubated at 30oC for 6 days to be the main parameters influencing the enzyme production. Of these factors, four variables including soyabean meal, FeSO4, MnSO4 and NaNO3 were chosen to study the interactive effects and their optimum levels in central composite design of response surface methodology with the final mannanase yield of 193 IU/gds. The kinetic characterization revealed the crude enzyme to be active over broader temperature and pH range. This could result in 26.6% reduction in kappa number with 4.93% higher tear index and 1% increase in brightness when used to treat the wheat straw based kraft pulp. The hydrolytic potential of enzyme was also demonstrated on both locust bean gum and guar gum.

Keywords: Brewer’s Spent Grain, Fusarium oxysporum, Mannanase, Response Surface Methodology.

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Authors: A. Abbas Khalaf, L. Issazadeh, Z. Arif Abdullah, J. Hassanpour

Abstract:

In order to evaluate the growth and yield properties of two Sorghum-Sudangrass hybrids under different irrigation levels, an investigation was done in the experiment site of Collage of Agriculture, University of Duhok, Kurdistan region of Iraq (36°5´38^⸗ N, 42°52´02^⸗ E) in the years 2015-16. The experiment was conducted under Randomized Complete Block Design (RCBD) with three replications, which main factor was irrigation treatments (I₁₀₀, I₇₅ and I₅₀) according to evaporation pan class A and type of Sorghum-Sudangrass hybrids (KH12SU9001, G₁) and (KH12SU9002, G₂) were factors of subplots. The parameters studied were: plant height (cm), number of green leaves per plant; leaf area (m²/m²), stem thickness (mm), percent of protein, fresh and dry biomass (ton.ha^-1) and also crop water productivity. The results of variance analysis showed that KH12SU9001 variety had more amount of leaf area, percent of protein, fresh and dry biomass yield in comparison to KH12SU9002 variety. By comparing effects of irrigation levels on vegetative growth and yield properties, results showed that amount of plant height, fresh and dry biomass weight was decreased by decreasing irrigation level from full irrigation regime to 5 _o% of irrigation level. Also, results of crop water productivity (CWP) indicated that improvement in quantity of irrigation would impact fresh and dry biomass yield significantly. Full irrigation regime was recorded the highest level of CWP (1.28-1.29 kg.m^-3).

Keywords: Deficit irrigation, growth, Sorghum-Sudangrass hybrid, yield.

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