Homology modeling of pyranose 2-oxidase from phanerochaete chrysosporium

Currently, most of the demand for energy relies on petroleum products. Nevertheless, the issues of energy security, economics and environment has led to the breakthrough of biofuel cells (BFCs) technology as one of the promising solution to the problems. However, the performance of BFCs need to be improved in order to compete with the existing technologies. One way to improve the efficiency of BFCs is to ensure that the enzyme used as the catalyst in BFCs, in this case, pyranose 2-oxidase (P2Ox) has better binding characteristic and more reactive. For this purpose, studies on three-dimensional (3-D) structure of P2Ox enzyme can offer insights on the structure-function correlations. Unfortunately, at present there is no available crystal structure of P2Ox from Phanerochaete chrysosporium (PcP2Ox). Thus, in this study homology modelling was used as the reliable alternative method to predict the 3-D structure of PcP2Ox enzyme and thus provide necessary information to improve the efficiency of the enzyme

Molecular dynamics approach in designing Thermostable Bacillus circulans Xylanase

We have applied molecular dynamics methods as a tool in designing thermostable Bacillus circulans Xylanase, by examining Root Mean Square Deviation (RMSD) of enzymes structure at its optimum temperature and compare with its high temperature behavior. As RMSD represents structural fluctuation at a particular temperature, a better understanding of this factor will suggest approaches to bioengineer these enzymes to enhance their thermostability. In this work molecular dynamic simulations of Bacillus circulans xylanase (BcX) have been carried at 318K (optimum catalytic temperature) and 343K (BcX reported inactive temperature). Structural analysis revealed that the fluctuations of the β-sheet regions are larger at higher temperatures compared to the fluctuations at optimum temperature

Ethical issues in environmental management and resource conservation from Islamic perspective

Environmental philosophy based on the Qur'an and Prophetic Traditions (Sunnah) is that there is a fundamental link and interdependency between all natural elements which is based on the premise that if man abuses or exhausts one element, the natural world as a whole will suffer direct consequences. The holistic principle of environmental management as applied by the Prophet Muhammad (SAW) is based on three important principles made up of the concepts of tawhid (unity), khilafah (stewardship) and amanah (trustworthy). The Islamic approach to maintaining a balance bet\veen material development and responsibility will be explored as applied in resource conservation and sustainability. The utilization of all natural resources - land, water, air, fire (energy)- forests, oceans - are considered the right and the joint property of the entire humankind and all creation of Allah on earth. Since Man is Khalifatullah (the vicegerent of Allah) on earth, he should take every precaution to ensure the interests and rights of others, and regard his mastery over his allotted piece of land as a joint Ownership with the next generation. Furthermore the Islamic nation has been tenned as (1/111111atan lvasatan) the moderate nation in the Qur'an, a nation that avoids excesses in all things. Thus, Muslims in particular have to utilize the resources provide on earth by Allah (S WT) responsibly for their benefit, honestly maintain and preserve it- use it considerately and moderately, and pass it on to future generations in an excellent condition

NGS-data analysis for netagenome cellulose- and Xylan- degrading enzymes finding

Abstract. For the aim of finding cellulose- and xylan-degrading enzymes needed in green industry to produce biofuel from plant biomass, a metagenomic DNA library from palm oil mill effluent (POME) was constructed and high-throughputly screened. The positive clones’ DNA were sequenced with next generation sequencing and raw data (short insert-paired) was analyzed with bioinformatic tools. First, the quality of 64.821.599 reverse and forward sequences of 101bp length raw data was identified using Fastqc. Then, raw data filtering was done by trimming low quality values and short reads and the vector sequences were removed and again the output was checked and the trimming was repeated until a high quality read sets was obtained. The second step was the de novo assembly of sequences to reconstruct 2900 contigs following de bruijn graph algorithm. Pre-assembled contigs were arranged in order, the distances between contigs were identified and oriented with SSPACE, where 2139 scaffolds have been reconstructed. 16386 genes have been identified after gene prediction using Prodigal and putative ID assignment with Blastp Vs NR protein. In these results, 17 cellulose-degrading enzymes and 2 xylan-degrading enzymes have been found. The genes encoding these enzymes will be recombinant to pBAD TOPO vector and cloned into TOP10 E. coli to express and characterize the enzymes for downstream processes. Key words: metagenomics, contig, scaffold, de novo assembly, de Bruijn, SSPACE, Prodigal, Blastp

Mechanical improvement of halal gelatin from marine sources

Gelatin replacement has existed for many years for the vegetarian, halal and kosher markets, but has gained increased interest in the last decade, particularly within Europe with the emergence of bovine spongiform encephalopathy or as known as mad cow disease. Since most commercial gelatins are obtained from either pigskin or cow hide, there has been considerable interest in finding and using alternative substitutes. Hence, extracting gelatin from fish skin as new source of gelatin is highly granted. In this research, two types of marine sources were examined for the highest value of gel strength and viscosity under three mechanical improvement conditions using enzyme transglutaminase, namely, incubation temperature, incubation time, and enzyme concentration. The extracted sample that has excellent gel strength were selected for the optimization of the modification conditions by using Central Composite Design (CCD) by Design Expert v.6.0.8. Hexanchus griseus or shark was found to have the highest value of gel strength which are 2.6g. The analysis revealed that the maximum gel strength from gelatin extract of Hexanchus griseus skin can be reached with these conditions: 6°C, 24 hr and 0.15mg/ml of enzyme concentration

Mechanical properties of a gelatin replacer, pectin, from banana and mango peels

An experimental design was used to slUdy the influence of pH, tempemture and time on the extraction of pectin from banana peels (Musa) and mango peels (Mungiferu indica), The yield of the extracted pcetin was measured to dctermine the optimum extraction condition. Alcohol insoluble solid (A1S) method was used for the extraction technique where ethanol was the solvent. The design of experiment WaS performed using statistical software Design Expen to know the pattern on the experiment C"Onducted. The tcmperarure, pH and time of extraction of AIS were optimiud using 2-faetorial design. Statistical analysis showed that the optimum parameters that provided the maximum pectin yields were at 4 hours. pH 2.0 and 9O"C of extraction. The pectin yields from both banana and mango peels were measured and calculated to be within the r,mge of 53 to 134 mglg aod 58 to 122 mglg respectively

A new isolate of thermophilic and organic solvent tolerant bacteria for lipase production using basal medium of palm kernel cake

Aims: This research focused on the selection of potential strains especially bacteria that can grow effectively in palm kernel cake (PKC) and produce high amount of thermostable and solvent tolerant (TS-OST) lipase. The work involved the exploration of renewable PKC as potential fermentation medium for discovery to novel TS-OST lipase that would have excellent tolerance and activity in presence of organic solvents with high temperatures for industrial applications. Methodology and results: Using palm kernel cake (PKC) as source of thermophilic bacteria, 53 bacterial strains were found survived at temperature 65 °C. However, after subcultured several times, only 17 strains were found as pure thermophilic strains. Preliminary screening both qualitative and quantitative was performed to all 17 potential thermophilic bacterial strains and showed that only 11 purified thermophilic strains are lipase producer. Strain PKC-P1 produced highest enzyme activity (11.13 U/g), followed by PKC-P13 and PKC-C9. The lowest enzyme activity was lipase produced byPKC-C10 (0.76U/g). Strain PKC-P1 has been classified as Gram negative bacteria and identified as Bacillus smithii strain PKC_P1. Conclusion, significance and impact of study: PKC as a by-product of oil palm industry consists of many nutrients that can give benefits towards industry and can be utilized in order to produce enzymes like lipases. From these results, it could be concluded that this lipase stable at temperature 65 °C and pH 7 and may be a potential candidate to be used in a variety of biotechnological applications. This finding revealed that a bacterial strain obtained from oil-rich environment which is PKC through isolation process has potential as a source of more economical enzyme to be applied in biotechnology industry. © 2018

Physico-chemical properties of collagen extracts from two local fish species

Production of high quality gelatin from Labeo rohilO (rohu) skill alld Megalaspis cordyla (torpedo scad) skill and scale as an ahemmive of porcine and bovine gelatin has beell conducted through modificatioll process using transglutaminase. Screening showed that Labeo rohila (rohu) skiJl has a beller quality of gelatiJl with the maximum gel strength and viscosity valucs aftcr the modification. The gel strength is 114.70g with TGase addition while the viscosity is 0.01960 Pa. The resulls of this study suggest that transglutaminase concemration. incubation time alld incubation temperature affect the gel strength and viscosity of the gelatill produced, Central composite Design (CeO) from Design Expert was applied to determille the optimal conditions for the modification for thc highest values of gel strength. The optimum modification conditions were attained at 6·C incubation temperature for 24h incubation time and TGase concentration is 0.1 Sgfml. The gelatin obtained from these conditions is 10.7Ig

Modification and characterization of phytases for animal feed production

Phytases catalyze the hydrolysis of inorganic phosphate from phytic acid and improve the nutritional quality of phytate rich diet. Monogastric animal such as poultry and fish do not have the ability to completely hydrolyze phytate. As a result, beneficial nutrient necessary for growth becomes unavailable and its elimination through excretions leads to land pollution, eutrophication of ground water and aquatic environment. Besides, it leads to the negative effect on vitamin utilization that lead to the emaciation, retarded growth and reproductive failure in animals. In view of these adverse effects phytases are added in animal feeds. Phytases from microbial sources are commonly used for their commercial exploitations. Waste water bacterium phytase is the subject of interest in this project. In the present study in-silico experiments are used to identify and examine active site of phytase.The factors influencing the ligand binding strength in the active site is analyzed and computational site directed mutagenesis experiments have been carried out to evaluate the effects of mutations on the binding strength. Compare to native enzyme, structural prediction suggest that single mutations at position M216R and E219R add hydrogen bonds surrounding the active site, which increases in the binding of the phytate substrate eventually leading to better degradation. Detailed results from out single and multiple mutation studies provide new direction towards design and development of new phytases with enhanced functional properties