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

Thermostable and organic solvent tolerant lipase producing fungi in solid state bioconversion of palm kernel cake

Lipase possessing thermal stability and organic solvent tolerant are believed to distinctively enhance lipase-catalyzed reactions of industrial importance. This study sought to explore the potential of palm kernel cake (PKC) to act as an oil and lipid rich environment for fungal growth, as well as a substrate to produce thermostable and organic solvent tolerant lipase through solid-state bioconversion. Four thermal and solvent tolerant fungi have successfully isolated with lipase producing capabilities. The isolates were screened based on the clearing zone methods on phenol red as well as on tween 80 agar media and quantified using solid-state bioconversion. Among the four isolates, PKC12B2 displayed highest clearance zone on the plate and lipase activities with 5.83 U/gram dry PKC. Morphological identification of PKC12B2 showed the characteristic of genus Rhizopus sp

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

A comparative study on male rape in Malaysia and other jurisdictions / Adzim Amir Hamzah, Suzalena Salleh and Azmahanim Azman Shah

For the last two semesters we have been conducting a research on the law of male rape in Malaysia and other jurisdictions namely in United Kingdom, United States, Singapore and Australia. In our research we concentrated on both form of the crime which is sodomy and female raping male issue. Seemingly, the latter form of male rape is being taken lightly around the world. Nonetheless we found that the law of sodomy is getting the recognition it deserved although the development has been slow and still in some area, insufficient. Therefore it is fundamental for a research to be conducted on this topic. The importance of enacting such laws therefore can be analyzed as a whole. In Malaysia, we have tried to analyze and discuss Section 377 of the Penal Code thoroughly in order to ascertain its effectiveness in combating the crime of sodomy. The result is in the negative. Thus, amending the section or enacting a new and more extensive law is practical and much needed. In completing our project paper, we have distributed questionnaires concerning male rape to 400 respondents. The outcome of the questionnaires is as we expected. A majority of the respondents is aware of such crime but still obscure regarding the law that govern the offence. Among the important questions that were asked in the questionnaires was whether the respondents are aware that a female rapist may escape scot-free from the crime of male rape and whether a specific provision on male rape should be enacted in the Penal Code. We benefited a lot from the answers that we managed to gather through the questionnaires. However, our research is also based on our readings of various books and materials that we find in online. After two semesters, we finally finished doing our project paper on a comparative study on the law of male rape in Malaysia and other jurisdictions