Mechanistic behaviour and molecular interactions of heat shock protein 47 (HSP47)

This project involves the study of heat shock protein 47 (HSP47), which is a molecular chaperone crucial for collagen biosynthesis. It exhibits a high degree of sequence homology with members of the serine protease inhibitor (serpin) superfamily, though HSP47 does not possess the inhibitory activity. It is a single-substrate chaperone, and binds only to collagen. ‘Knock-out’ of the hsp47 gene impairs the secretion of correctly folded collagen triple helix molecules leading to embryonic lethality in mice. Thus the aim of this project was to elucidate the specific mechanism that governs the binding to and release from collagen at the molecular level, known as the ‘pH-switch mechanism’. Emphasis is given on histidine (His) residues as the HSP47-collagen dissociation pH is similar to the pKa of the imidazole side chain of His residues. Site directed mutagenesis was used to mutate surface His residues, based on a mouse HSP47 homology model. The effects of the mutations on the behaviour of HSP47 were then assessed by collagen binding assays and structural analyses with circular dichroism (CD). All mutants were found to have good solubility and retain their binding ability to collagen like wild-type HSP47 in batch assay, but perturbed behaviour was seen in column experiment. Mutation of His residue at position 191 (H191) causes the shift in the collagen dissociation pH, while mutation of H197 and/or 198 disrupt the specific HSP47-collagen interaction. H191, 197 and 198 are predicted to be located in the region near the C-terminus of strand 3 of β-sheet A (s3A) in the homology model, a region specifically known as the ‘breach cluster’ in serpin nomenclature. The extent of conformational rearrangement of this region was further investigated by means of intrinsic tryptophan fluorescence spectroscopy using a series of single tryptophan (Trp) mutants. Results from analyses performed on the mutants did not contradict the observation seen in His mutational work, as Trp residues in the ‘breach’ cluster are likely to be located in the dynamic region of HSP47 pH-triggered conformational change. In conclusion, this study establishes the importance of His residues in the ‘breach cluster’ to HSP47 pH-switch behaviour. Finally, a model for HSP47 pH-switch mechanism was proposed from data obtained via mutagenesis experiments. The model is hoped to assist future research into HSP47 cellular behaviour and will also be of great use in therapeutic applications involving the molecular chaperone

Taking on Diplomacy Role as a Scientist: A Personal Reflection and What Next?

13-16I have always had a broad interest in various areas from when I was little. I remember spending time in the school library reading books on all sorts of topics, from astronomy to geography, arts, history, architecture, and of course science

Zinc-air cell employing laccase as the oxygen reduction catalyst

Zinc-air cell employing laccase enzyme as the oxygen reduction catalyst has been investigated. Laccase is an oxidoreductase, belongs to the copper-containing enzyme family which attracts many due to its ability to reduce molecular oxygen to water. The test cell consisted of zinc metal foil as the anode and a carbon-based air electrode as the cathode, encapsulated in a single chamber, home-made acrylic board casing. The electrolyte composed of laccase and syringaldazine in a potassium dihydrogen phosphate buffer. The performance of the cell was also evaluated using sodium citrate buffer and potassium citrate buffer. Zinc-air cell utilizing laccase biocatalyst registered an open circuit voltage of 1.2 V and was able to sustain a discharge load of 500 A

EXPRESSION AND ENZYMATIC PROPERTIES OF A UNIQUE RECOMBINANT ANTICOAGULANT AND FIBRINOLYTIC ENZYME FROM ACINETOBACTER BAUMANNII TU04

Objective: The objective of this research is to clone and express a new fibrinolytic enzyme encoding serine protease gene in Escherichia coli thus, characterize such purified recombinant.Methods: The recombinant clone was successfully expressed in Lemo21 system and purified using immobilized nickel cation affinity chromatography on a His•bind resin®, followed by ammonium sulfate precipitation and protein filtration in combination. General properties of the purified enzyme were investigated, including the molecular weight, effects of inhibitors and metal ions, substrate specificity, amylolytic activity, fibrinolytic activity and effect of anticoagulant activity in-vitro.Results: The recombinant clone was expressed in Lemo21 system in the cytoplasm in a soluble and active form. The resulting enzyme, SERpro was purified to homogeneity with a purification of 19.35-fold and recovery yield of 4.85%. The enzyme exhibited maximal activity at 37 °C and at pH7.4, respectively. The molecular weight of the purified enzyme was 82 kDa, determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The fibrinogenolysis peptide sequence analysis revealed that SERpro degraded Bβ chain of Fibrin at a much lower rate but cleaved Aα and γ-chain extensively. The enzyme was activated by metal ions such as Mg2+, Fe3+and Zn2+, and was inhibited strongly by PMSF. The clotting time of human blood serum in the presence of 1U SERpro reached a relative partial thromboplastin time of 13.9% with a 1.14-fold increase.Conclusion: The study deduced SERpro as a new protease with anti-thrombotic activity from Acinetobacter baumannii TU04.Â

Biomolecular aspects of second order limit language

The study on the recombinant behavior of double-stranded DNA molecules has led to the mathematical modelling of DNA splicing system. The interdisciplinary study is founded from the knowledge of informational macromolecules and formal language theory. A splicing language is resulted from a splicing system. Recently, second order limit language, a type of the splicing language, has been extensively explored. Before this, several types of splicing languages have been experimentally proven. Therefore, in this paper, a laboratory experiment was conducted to validate the existence of a second order limit language. To accomplish it, an initial strand of double-stranded DNA, amplified from bacteriophage lambda, was generated through polymerase chain reaction to generate thousands of copies of double-stranded DNA molecules. A restriction enzyme and ligase were added to the solution to complete the reaction. The reaction mixture was then subjected to polyacrylamide gel electrophoresis to separate biological macromolecules according to their sizes. A mathematical model derived at the early study was used to predict the approximate length of each string in the splicing language. The results obtained from the experiment are then used to verify the mathematical model of a second order limit language. This study shows that the theory on the second order limit language is biologically proven hence the model has been validated

Microbiological analysis of drinking water from water vending machines

Commercial water vending machines are gaining popularity nowadays among the general public, probably due to the ease of obtaining clean drinking water. However, improper maintenance of the machines can lead to bacterial contamination. Hence, this study aimed to investigate and determine the microbiological characteristics of drinking water from Water Vending Machines (WVM) by isolating and characterizing culturable bacteria in the water and nozzle swab samples. The samples were obtained from WVM at eight different locations around Johor Bahru, Johor, Malaysia. Several unique bacterial isolates were found, from both Gram-positive and Gram-negative groups. Polymerase chain reaction amplification and 16S rRNA sequence analysis suggested that these isolates are from Pseudomonas, Bacillus, and Stenotrophomonas genera. In situ water quality tests which include pH, conductivity, and total dissolved solids were also conducted. Two samples from the inlet source have pH and conductivity values slightly above the reference values stipulated in drinking water regulations. The findings presented here suggest the importance of regular service maintenance of the WVM to ensure that the water samples meet the standard stipulated by the authority

Predictive modelling of marine fish landings in Malaysia

The fisheries sector plays an important role in the economy as a major source of food, employment and income in Malaysia. In this study, the future number of marine fish landings in Malaysia will be predicted. The monthly data from January 2005 until December 2014 were taken from Department of Fisheries Malaysia, Ministry of Agriculture and Agro-Based Industry Malaysia. The aims of this study are to predict the landing of marine fish in Malaysia by using Box-Jenkins and HoltWinters and to make a comparison between two models in order to find the better model for prediction of marine fish landings in Malaysia. Data for the number of marine fish landings is a trend pattern. Box-Jenkins and Holt-Winters approach will be applied to the number of marine fish landings. In this study, the forecast accuracy of Box-Jenkins and Holt-Winters approach has been compared by using the mean square error (MSE) and mean absolute percentage error (MAPE). The better model obtained from Box-Jenkins approach was SARIMA(2, 1, 0)(0, 1, 1)12. For Holt-Winters, additive model is chosen since the MSE and MAPE values are lower. After comparing the Box-Jenkins approach and additive Holt-Winters, it is found that additive Holt-Winters is a better method with a lower value of MSE and MAPE and could be used by fisheries managers and scientists to decide on sustainable management issues

Reduction of cogging torque of single phase brushless DC motor using flux barrier

This paper deals with the reduction of cogging torque in a single phase brushless DC motor. The constructional features and operating principles of the developed motor is presented. Reduction of the cogging torque is achieved by the use of slit as flux barrier. By using slit to stable the flux density of the motor, the cogging torque produced by the motor is reduced. Simulation studies to evaluate the aspects of the flux distribution inside the machine and the cogging torque characteristic are presented

Bantuan pembelajaran mengenal warna menggunakan tipografi bagi kanak-kanak rabun warna / Intan Nur Firdaus Muhammad Fuad, Khairul Nizan Mohd Aris dan Mohd Salleh Abdul Wahab

Warna memainkan peranan penting dalam kehidupan kita dimana warna sering digunakan untuk menentukan dan mempengaruhi emosi dan tindakan kita. Warna terhasil dari getaran cahaya. Warna hadir di sekeliling kita dan terlibat dalam setiap aspek kehidupan kita. Mata manusia yang dicitakan olehNYA dijadikan bijak mengesan warna. Kadang-kadang, pilihan warna mempengaruhi dan mencerminkan keperibadian dan pemikiran kita. Namun dalam mengenal warna. Ia menjadi masalah buat mereka yang menghidapi rabun warna. Kesan warna pembalikan cahaya pada objek yang dapat dikesan melalui gangguan visual atau deria. Tanpa cahaya kita tidak dapat melihat warna. Oleh itu, warna dan cahaya adalah dua perkara yang berkaitan rapat yang membuat manusia dapat mengesan warna. Tetapi masalah buta warna adalah gangguan yang disebabkan oleh ketidakupayaan sel-sel kerucut mata untuk menangkap spektrum warna tertentu yang disebabkan oleh faktor genetik. Ini membawa maksud bahawa masalah rabun warna ia kongenital iaitu terjadi dari sejak lahir lagi dan masalah ni tiada lagi alat atau ubat yang boleh membantu kesembuhannya. Sesetengahnya tidak akan sedar mereka pengidap ketidakupayaan ini sehingga lah mereka dewasa. Dalam kajian ini Kehadiran suatu konsep sistem sokongan dilihat amat penting dalam membantu kanak-kanak tersebut mentafsir warna. Oleh yang sedemikian peranan tulisan ataupun tipografi dilihat amat penting. Sistem ini dilihat lebih mudah diadaptasi dan digunapakai bukan sahaja membantu kanak-kanak yang menghidapi ketidakupayaan ini tetapi juga ia dilihat dapat membantu kanak-kanak lain dalam belajar mengenal warna, seperti kita sedia maklum perkembangan kanak-kanak dapat berlaku melalui banyak melakukan aktiviti mewarna. Setiap perkembangan yang baik ini adalah amat penting bagi kesemua kanak-kanak. Dan kanak-kanak yang tidak mempunyai kemahiran atau kekeliruan dalam mengenal warna ini seharusnya tidak boleh ketinggalan. Sistem mengenal warna yang mudah ini dilihat memainkan peranan yang penting dalam membantu kanak-kanak tersebut meningkatkan perkembangan mereka

Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook

Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Understanding of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome-based technologies and knowledge can be used effectively in biohydrogen production systems, in order to maximise the production output