Lubna Kamil Abdulhussein Abo-Shakeer, M. H. Yakasai, M. F. Rahman, N. A. Bakar, M. Syed, N. Abdullah, A. Othman
{"title":"Partial purification of the molybdenum-reducing enzyme from Bacillus pumilus strain Lbna","authors":"Lubna Kamil Abdulhussein Abo-Shakeer, M. H. Yakasai, M. F. Rahman, N. A. Bakar, M. Syed, N. Abdullah, A. Othman","doi":"10.54987/bstr.v4i1.366","DOIUrl":"https://doi.org/10.54987/bstr.v4i1.366","url":null,"abstract":"Molybdenum is an emerging pollutant. Bioremediation of this heavy metal is possible by the mediation of Mo-reducing bacteria. These bacteria contain the Mo-reducing enzymes that can conver toxic soluble molybdenum into molybdenum blue; a less soluble and less toxic form of the metal. To date only the enzyme has been purified from only one bacterium. The aim of this study is to purify the Mo-reducing enzyme from a previously isolated Mo-reducing bacterium Bacillus pumilus strain Lbna using ammonium sulphate fractionation followed by ion exchange and then gel filtration. Two clear bands were obtained after the gel filtration step with molecular weights of 70 and 100 kDa. This indicates that further additional purification methods need to be used to get a purified fraction. Hence, additional steps of chromatography such as hydroxyapatite or chromatofocusing techniques can be applied in the future.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125453636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Siti Nur Khadijah Jamulidin, M. Manogaran, M. H. Yakasai, M. F. Rahman, M. Shukor
{"title":"Partial purification and characterization of the molybdenum-reducing enzyme from the glyphosate-degrading Burkholderia vietnamiensis strain AQ5-12","authors":"Siti Nur Khadijah Jamulidin, M. Manogaran, M. H. Yakasai, M. F. Rahman, M. Shukor","doi":"10.54987/bstr.v4i1.363","DOIUrl":"https://doi.org/10.54987/bstr.v4i1.363","url":null,"abstract":"In this study, a novel glyphosate-degrading shows the ability to reduce molybdenum to molybdenum blue. The enzyme from this bacterium was partially purified and partially characterized to ascertain whether the Mo-reducing enzyme from this bacterium shows better or lower efficiency in reducing molybdenum compared to other Mo-reducing bacterium that only exhibits a single biotransformation activity. The enzyme was partially purified using ammonium sulphate fractionation. The Vmax for the electron donating substrate or NADH was at 1.905 nmole Mo blue/min while the Km was 6.146 mM. The regression coefficient was 0.98. Comparative assessment with the previously characterized Mo-reducing enzyme from various bacteria showed that the Mo-reducing enzyme from Burkholderia vietnamiensis strain AQ5-12 showed a lower enzyme activity.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"55 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131798013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abubakar Aisami, Allamin Ibrahim Alkali, N. A. Yasid
{"title":"Phenol removal via cellular immobilization: A mini review","authors":"Abubakar Aisami, Allamin Ibrahim Alkali, N. A. Yasid","doi":"10.54987/bstr.v4i1.362","DOIUrl":"https://doi.org/10.54987/bstr.v4i1.362","url":null,"abstract":"Phenolic compounds or phenols are a group of aromatic compounds that comprises a hydroxyl group (OH) that is directly bonded to an aromatic ring. Phenols are injurious to organisms even at even low concentrations with many of them are categorized as dangerous pollutants because of their likely harm to human well-being. This review attempts to discuss the various merits and demerits of immobilization matrices employed for phenol-degrading microorganisms’ immobilization. One of several key points of cellular immobilization is the capacity to protect bioremediation agents towards toxic levels of specific toxicants and safeguarding from predatory microorganisms. However, this shielding course of action should never impede the diffusion of substrates into the pores of the immobilization structure. In the end the choice of a particular immobilization method will strongly hinge on aspects of economy, safety and efficacy.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114167947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bartlett and the Levene’s tests of homoscedasticity of the modified Gompertz model used in fitting of Burkholderia sp. strain Neni-11 growth on acrylamide","authors":"A. Shukor, M. Yunus","doi":"10.54987/bstr.v4i1.367","DOIUrl":"https://doi.org/10.54987/bstr.v4i1.367","url":null,"abstract":"Most often than not, microorganism’s growth curve is sigmoidal in characteristics. The modified Gompertz model via nonlinear regression using the least square method is one of the most popular methods to describe the growth curve. One of the assumptions of a good model is that the variance of the data must be homogenous (homoscedasticity). In this work, two statistical diagnostics; the Bartlett and the Levene’s tests was performed to a modified Gompertz model utilized to model the growth of the bacterium Burkholderia sp. strain Neni-11 on acrylamide in order to satisfy the requirement above and found that data conformed to the requirement indicating the modified Gompertz model is a robust model for modelling the bacterial growth process.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116464544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Halmi, B. Gunasekaran, A. Othman, K. Kamaruddin, F. Dahalan, N. Ibrahim, M. Shukor
{"title":"A rapid inhibitive enzyme assay for monitoring heavy metals pollution in the Juru Industrial Estate","authors":"M. Halmi, B. Gunasekaran, A. Othman, K. Kamaruddin, F. Dahalan, N. Ibrahim, M. Shukor","doi":"10.54987/bstr.v3i2.290","DOIUrl":"https://doi.org/10.54987/bstr.v3i2.290","url":null,"abstract":"The volume of contaminated rivers in Malaysia continues to keep rising through the years. The cost of instrumental monitoring is uneconomical and prohibits schedule monitoring of contaminants particularly heavy metals. In this work, a rapid enzyme assay utilizing the molybdenum-reducing enzyme as an inhibitive assay, prepared in crude form from the molybdenum-reducing bacterium Serratia sp. strain DRY5 has been developed for monitoring the heavy metals mercury, silver, copper and chromium in contaminated waters in the Juru Industrial Estate. The crude enzyme extract transformed soluble molybdenum (phosphomolybdate) into a deep blue solution, which is inhibited by heavy metals such as mercury, silver, copper and chromium. The IC50 and Limits of Detection (LOD) values for mercury, copper, silver and cadmium were 0.245, 0.298, 0.367, 0.326, and 0.124, 0.086, 0.088 and 0.094 mg L-1, respectively. The assay is rapid, and can be carried out in less than 10 minutes. In addition, the assay can be carried out at ambient temperature. The IC50 values for these heavy metals are more sensitive than several established assays. Water samples from various locations in the month of November from the Juru Industrial Estate (Penang) were tested for the presence of heavy metals using the developed assay. Enzyme activity was nearly inhibited for water samples from several locations. The presence of heavy metals was confirmed instrumentally using Atomic Emission Spectrometry and a Flow Injection Mercury System. The assay is rapid and simple and can be used as a first screening method for large scale monitoring of heavy metals.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"98 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114695878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. K. Sabullah, M. Shukor, Azlan Jualang Gansau, B. Gunasekaran, N. A. Shamaan, M. R. Sulaiman
{"title":"Observation of the bile canaliculi of Puntius javanicus liver affected by copper","authors":"M. K. Sabullah, M. Shukor, Azlan Jualang Gansau, B. Gunasekaran, N. A. Shamaan, M. R. Sulaiman","doi":"10.54987/bstr.v3i2.298","DOIUrl":"https://doi.org/10.54987/bstr.v3i2.298","url":null,"abstract":"Investigation on in vivo effects of copper (Cu) on the ultrastructure of P. Javanicus liver was carried out using transmission electron microscopy (TEM). The addition of sublethal concentration of 5 mg/L of Cu caused abnormalities on the bile canaliculi (BC) including dilation and elongation compared to control and at lower concentrations of copper with a normal round shape form. Findings from this study support an alternative histological assessment of the effects of Cu concentration on P. Javanicus liver.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"79 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133387369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Othman, I. Zeid, M. F. Rahman, Fazilah Ariffin, M. Shukor
{"title":"Isolation and characterization of a molybdenum-reducing and orange G-decolorizing Enterobacter sp. strain Zeid-6 in soils from Sudan","authors":"A. Othman, I. Zeid, M. F. Rahman, Fazilah Ariffin, M. Shukor","doi":"10.54987/bstr.v3i2.295","DOIUrl":"https://doi.org/10.54987/bstr.v3i2.295","url":null,"abstract":"Chemical toxins and organic contaminants such as hydrocarbons and dyes are major global contaminants with countless tones of those chemicals are created yearly with a significant amount release to the environment. In this work we screen the ability of a molybdenum-reducing bacterium isolated from contaminated soil to decolorize various azo and triphenyl methane dyes independent of molybdenum reduction. Biochemical analysis resulted in a tentative identification of the bacterium as Enterobacter sp. strain Zeid-6. The bacterium was able to decolorize the azo dye Orange G. The bacterium reduces molybdate to Mo-blue optimally at pH between 5.5 and 8.0 and temperatures of between 30 and 37 oC. Other requirements include a phosphate concentration of 5 mM and a molybdate concentration of 20 mM. The absorption spectrum of the Mo-blue produced was similar to previous Mo-reducing bacterium, and closely resembles a reduced phosphomolybdate. Molybdenum reduction was inhibited by copper, lead, mercury and silver which showed 36.8, 16.9, 64.9 and 67.6% inhibition to Mo-reducing activity of Enterobacter sp. strain Zeid-6, respectively. The resultant molybdenum blue spectrum closely resembles the spectrum of molybdenum blue from the phosphate determination method. The ability of this bacterium to detoxify molybdenum and decolorize azo dye makes this bacterium an important tool for bioremediation.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"221 5177 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129191926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bacillus thuringiensis subsp. Entomocidus HD9 Cry1Ba4 insecticidal crystal protein: In-silico mutation, cloning, expression, mutation and domain I functional study","authors":"Mohd Fadzli Ahmad, H. Abdullah","doi":"10.54987/bstr.v3i2.296","DOIUrl":"https://doi.org/10.54987/bstr.v3i2.296","url":null,"abstract":"The 3D structure of the insecticidal protein Cry1Ba4 produced by B. thuringiensis subsp. Entomocidus HD-9 was determined using homology modelling. From the model built, we have been able to identify the possible sites for structure modification by site-directed mutagenesis. The mutation was introduced at the conserved region of α-helix 7 by substituting the hydrophobic motif that comprises alanine 216, leucine 217 and phenylalanine 218 with arginine. Wild and mutant Cry1Ba4 genes were cloned into pET200/D-TOPO and expressed in the expression host. The result suggests that mutant Cry1Ba4 protein was less toxic to the larvae Plutella xylostella compared to the wild-type. In conclusion, alteration in the structure of Domain I had left an impact on the toxicity of Cry1Ba4 against P. xylostella.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124055973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. K. Sabullah, Fisal Ahmad, Azlan Jualang Gansau, M. R. Sulaiman
{"title":"A one dimensional PAGE studies on Puntius javanicus liver proteome affected by copper toxicity","authors":"M. K. Sabullah, Fisal Ahmad, Azlan Jualang Gansau, M. R. Sulaiman","doi":"10.54987/bstr.v3i2.297","DOIUrl":"https://doi.org/10.54987/bstr.v3i2.297","url":null,"abstract":"Observations on the effects of copper on the liver proteome of Puntius javanicus based on the one dimensional PAGE was carried out. The liver was dissected from each fish, which was separately treated with different concentrations of copper sulfate ranging from 0.1 to 5.0 mg/L. The livers were extracted and one dimensional PAGE was performed under nonreducing (native) and reducing (SDS)-PAGE. Several bands were resolved in the native PAGE with probable candidates for the effect of copper observed showing an increased in the expression and downregulation strongly associated with increasing copper concentrations. This study showed that high concentrations of copper significantly alters P. Javanicus liver at the proteome level, and preliminary screening based on one dimensional PAGE is considered rapid and simple to assess the toxicity effect of copper before more advanced and extensive assesment with a second dimensional PAGE is carried out.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122290825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mathematical modeling of molybdenum blue production from Serratia marcescens strain DR.Y10","authors":"A. Othman, W. Johari, F. Dahalan, M. Shukor","doi":"10.54987/bstr.v3i2.289","DOIUrl":"https://doi.org/10.54987/bstr.v3i2.289","url":null,"abstract":"The pollution of heavy metals and toxic xenobiotics has become a central issue worldwide. Bioremediation of these toxicants are being constantly carried out using novel microbes. Molybdenum reduction to molybdenum blue is a detoxification process and mathematical modelling of the reduction process can reveal important parameters such as specific reduction rate, theoretical maximum reduction and whether reduction at high molybdenum concentration affected the lag period of reduction. The used of linearization method through the use of natural logarithm transformation, although popular, is inaccurate and can only give an approximate value for the sole parameter measured; the specific growth rate. In this work, a variety of models for such as logistic, Gompertz, Richards, Schnute, Baranyi-Roberts, Von Bertalanffy, Buchanan three-phase and more recently Huang were utilized for the first time to obtain values for the above parameters or constants. The modified Gompertz model was the best model in modelling the Mo-blue production curve from Serratia marcescens strain DR.Y10 based on statistical tests such as root-mean-square error (RMSE), adjusted coefficient of determination (R2), bias factor (BF), accuracy factor (AF) and corrected AICc (Akaike Information Criterion). Parameters obtained from the fitting exercise were maximum Mo-blue production rate (um), lag time (l) and maximal Mo-blue production (Ymax) of X (h-1), Y (h) and Z (nmole Mo-blue), respectively. The application of primary population growth models in modelling the Mo-blue production rate from this bacterium has become a successful undertaking. The model may also be used in other heavy metals detoxification processes. The parameters constants extracted from this work will be a substantial help for the future development of further secondary models.","PeriodicalId":436607,"journal":{"name":"Bioremediation Science and Technology Research","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126998603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}