Displaying publications 1 - 20 of 37 in total

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  1. Noor Suffiah Md. Zin, Siti Nadzirah Padrilah, Mohd Fadhil Abd. Rahman, Koh, Sim Han, Ariff Khalid, Mohd. Yunus Shukor
    MyJurnal
    2,4-dinitrophenol (2,4-DNP) is utilized in the production of wood preservatives, dyes, and also
    as a pesticide. Human acute (short-term) exposure to 2,4-DNP in humans by means of oral
    exposure are nausea or vomiting, sweating, headaches, dizziness, and weight reduction. Thus, the
    removal of this compound is highly sought. A 2,4-DNP-degrading bacterium (isolate 1) was
    isolated from a sample soil from Terengganu. This bacterium (isolate 1) was characterized as a
    rod Gram positive, non-sporulated, and non-motile bacterium. The bacterium is oxidase negative
    and had catalase positive activity and was able to grow aerobically on 2,4-dinitrophenol as the
    sole carbon source. This bacterium showed maximal growth on 2,4-DNP at the temperature
    optimum of 30 oC, pH 5.0 and was tolerant to 2,4-DNP concentration of up to 0.5 mM (0.092
    g/L). This bacterium prefers to use urea as the nitrogen source in addition to yeast extract for
    mineral source and vitamin precursors.
  2. Yadzir, Z.H.M., Gafar, A.A., Rahman, M.F., Yakasai, M.H., Abdullah, M.A., Shamaan, N.A., et al.
    MyJurnal
    Contamination of organic xenobiotic pollutants and heavy metals in a contaminated site allows
    the use of multiple bacterial degraders or bacteria with the ability to detoxify numerous toxicants
    at the same time. A previously isolated SDS- degrading bacterium, Acinetobacter baumannii
    strain Serdang 1 was shown to reduce molybdenum to molybdenum-blue. The bacterium works
    optimally at pH 6.5, the temperature range between 25 and 34°C with glucose serves as the best
    electron donor for molybdate reduction. This bacterium required additional concentration of
    phosphate at 5.0 mM and molybdate between 15 and 25 mM. The absorption spectrum of the
    molybdenum blue obtained is similar to the molybdenum blue from other earlier reported
    molybdate reducing bacteria, as it resembles a reduced phosphomolybdate closely. Ag(i), As(v),
    Pb(ii) and Cu(ii) inhibited molybdenum reduction by 57.3, 36.8, 27.7 and 10.9%, respectively, at
    1 p.p.m. Acrylamide was efficiently shown to support molybdenum reduction at a lower
    efficiency than glucose. Phenol, acrylamide and propionamide could support the growth of this
    bacterium independently of molybdenum reduction. This bacterium capability to detoxify several
    toxicants is an important tool for bioremediation in the tropical region.
  3. Mohd. Yunus Shukor
    MyJurnal
    The growth of microorganism on substrates, whether toxic or not usually exhibits sigmoidal
    pattern. This sigmoidal growth pattern can be modelled using primary models such as Logistic,
    modified Gompertz, Richards, Schnute, Baranyi-Roberts, Von Bertalanffy, Buchanan threephase
    and Huang. Previously, the modified Gompertz model was chosen to model the growth of
    Burkholderia sp. strain Neni-11 on acrylamide, which shows a sigmoidal curve. The modified
    Gompertz model relies on the ordinary least squares method, which in turn relies heavily on
    several important assumptions, which include that the data does not show autocorrelation. In this
    work we perform statistical diagnosis test to test for the presence of autocorrelation using the
    Durbin-Watson test and found that the model was adequate and robust as no autocorrelation of
    the data was found.
  4. Roshani Othman, Sharr Azni Harmin, Ina-Salwany Md Yasin
    MyJurnal
    Mass production of fish broodstock with high quality eggs requires the knowledge on the chemical composition and physiochemical properties of vitellogenin (Vtg) during ovulation. Vtg is an egg yolk precursor phospholipoglycoprotein, and has been analysed to evaluate the reproductive conditions and determine the spawning period in captive and wild fish. In this study, Vtg was induced in male H. nemurus through three intramuscular injections of 17-estradiol (E2). The Vtg was purified from the serum using gel filtration chromatography and the purified protein was reduced via SDS-PAGE. One major polypeptide corresponding to 130 kDa was observed. Vtg identification was done using peptide mass fingerprint (PMF) from the trypsin digestion of male H. nemurus Vtg induced with E2. The sequence homology of H. nemurus AYLAGAAADVLEVGVR matched the Vtg of other fish species when analysed using MALDI-TOF. Vtg was confirmed by MASCOT at 95% significant level. The potential protein that controls the reproductive process and oocyte development isolated from this study was discussed to understand the structure and function of Vtg.
  5. Shukor, M.S., Shukor, M.Y.
    MyJurnal
    Quinolines compounds are toxic pollutants. Their biodegradation by microbes represents a tool
    for bioremediation. The growth of Klebsiella penumoniae on 2-methylquinoline shows typical
    sigmoidal bacterial growth curves. Since there exists a variety of models for describing the
    growth profile of microorganism such as logistic, Gompertz, Richards, Schnute, Baranyi-
    Roberts, Von Bertalanffy, Buchanan three-phase and more recently Huang models, the growth
    curves exhibit under such conditions would be an excellent study for finding the best model.
    The Huang model was chosen as the best model based on statistical tests such as root-meansquare
    error (RMSE), adjusted coefficient of determination (R2), bias factor (BF), accuracy
    factor (AF) and corrected AICc (Akaike Information Criterion). Novel constants obtained from
    the modelling exercise would be used for further secondary modelling.
  6. Mohd Aqmin Abdul Wahab, Adzleen Mohmood, Nur Khaliesah Jamadon, Amir Syahir
    MyJurnal
    The trend of global under-five child mortality rate showed a steady decrease at -3.14% per year
    approaching the United Nations millennium development goals target (-4.0% reduction per year
    from 1990-2015). This rate is usually inversely proportional to the nations GDP. However, the
    progress in the recent years (2006-2012) in Malaysia has raised a disturbing concern with an
    annual average increment of +0.81% per year. Thus, there is an urgent need to identify the
    reasons of such risky ecosystem. By analyzing recorded data on river pollution from 2007-
    2012, we found that river pollution has high correlation with the gross domestic products, not at
    the same year, but for two years prior that indicates a lag time. We also found that under-five
    child mortality has strong correlation with the river pollutions. The development-pollutionhealth
    triangular cycle needs to be put in a balanced to ensure the nation prosperity and
    sustainability of the nation.
  7. Wan Noraina Atikah Wan Mohd Musdek, Mohd Khalizan Sabullah, Nor Mustaiqazah Juri, Norliza Abu Bakar, Noor Azmi Shaharuddin
    MyJurnal
    Bioremediation is a new green economic approach in providing solutions for cleaning up
    contaminated sites. Phytoremediation uses plants as a tool for remediation purposes. The usage
    of plant species offers higher potential solution to remediate heavy metal contaminated sites.
    This study aimed on screening potential plant species for phytoremediation of heavy metal
    contaminated water. The potential of three aquatic macrophytes species (Eichorrnia crassipes,
    Pistia stratiotes and Ipomoea aquatica) for chromium and nickel phytoremediations was tested.
    The plants were exposed for 10 days under hydroponic conditions in heavy metal contaminated
    water. E. crassipes showed the highest chromium and nickel concentrations in its biomass, 1.60
    and 2.40 μg/L respectively. Meanwhile, P. stratiotes had chromium and nickel concentrations
    detected at 0.89 and 0.081 μg/L, respectively; chromium and nickel concentrations of I.
    aquatica detected were, 0.49 and 0.08 μg/L, respectively. The ability of these plants to
    accumulate heavy metals and survived throughout the experiment demonstrates the potential of
    these plants to remediate metal-enriched water. Among the three tested aquatic plants, E.
    crassipes was proven to be the most suitable plant species that can phytoremediate heavy metal
    contaminated water followed by P. stratiotes and I. aquatica.
  8. Hasdianty Abdullah, Mohd Fadzli Ahmad, Farah Aula Mohd Fauzi, Nor Suhaila Yaacob, Abdul Latif Ibrahim
    MyJurnal
    Protein function depends greatly on its structure. Based on this principle, it is vital to study the
    protein structure in order to understand its function. This study attempts to build the predicted
    model of lipase gene in Rhodococcus sp. NAM81 using homology modelling method. The
    predicted structure was then used to investigate the function of protein through several
    bioinformatic tools. The DNA sequence of lipase gene was obtained from the Rhodococcus sp.
    NAM81 genome scaffold. Blastx analysis showed 100% identity to the target enzyme andthe
    appropriate template for homology modelling was determined using Blastp analysis. The 3D
    protein structure was built using two homology modelling software, EsyPred3D and Swiss
    Model Server. Both structures built obtained LGScore of greater than 4, which means they are
    extremely good models according to ProQ validation criteria. Both structures also satisfied the
    Ramachandran plot structure validation analysis. The predicted structures were 100% matched
    with each other when superimposed with DaliLite pairwise. This shows that both structure
    validation servers agreed on the same model. Structure analysis using ProFunc had found seven
    motifs and active sites that indicate similar function of this protein with other known proteins.
    Thus, this study has successfully produced a good 3D protein structure for the target enzyme.
  9. Mohd. Yunus Shukor
    MyJurnal
    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.
  10. Othman, A.R., Shukor, M.Y., Johari, W.L.W., Dahalan, F.A.
    MyJurnal
    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 (μm), 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 Moblue
    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.
  11. Halmi, M.I.E., Baskaran Gunasekaran, Othman, A.R., Shukor, M.Y., Kamaruddin, K., Dahalan, F.A., et al.
    MyJurnal
    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.
  12. Othman, A.R., Rahman, M.F., Shukor, M.Y., Abu Zeid, I.M., Ariffin, F.
    MyJurnal
    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.
  13. Mohd Fadzli Ahmad, Hasdianty Abdullah
    MyJurnal
    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 -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.
  14. Halmi, M.I.E., Khayat, M.E., Rahman, M.F.A., Gunasekaran, B., Masdor, N.A.
    MyJurnal
    In this work, a temporal monitoring work for heavy metals from an effluent discharge point in
    the Juru Industrial Estate was carried out using the protease extracted from garlic (Allium
    sativum) as the principal bioassay system. casein-Coomassie-dye binding assay method has
    utilized this purpose. The periodic sampling results for one day of a location in the Juru
    Industrial Estate showed temporal variation of copper concentration coinciding with garlic
    protease inhibition with the highest concentrations of copper occurring between 12.00 and 16.00
    hours of between 3 and 3.5 mg/L copper. The crude proteases extracted from Allium sativum
    successfully detect temporal variation of copper form this location. In conclusion, this assay
    method has the potential to be a rapid, sensitive, and economic inhibitive assay for the largescale
    biomonitoring works for the heavy metal copper from this area.
  15. Abo-Shakeer, L.K.A., Yakasai, M.H., Rahman, M.F., Syed, M.A., Bakar, N.A., Othman, A.R.
    MyJurnal
    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.
  16. Abubakar Aisami, Allamin Ibrahim Alkali, Nur Adeela Yasid
    MyJurnal
    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.
  17. Jamulidin, S.N.K., Manogaran. M., Yakasai, M.H., Rahman, M.F.A., Shukor, M.Y.
    MyJurnal
    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.
  18. Mohd Khalizan Sabullah, Azlan Jualang Gansau, Mohd Rosni Sulaiman, Fisal Ahmad
    MyJurnal
    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.
  19. Mohd Khalizan Sabullah, Azlan Jualang Gansau, Mohd Yunus Shukor, Baskaran Gunasekaran, Nor Arifin Shamaan, Mohd Rosni Sulaiman
    MyJurnal
    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.
  20. Siti Fadhilah Abd. Rahim, Normala Masrom, Muhamad Cyrill Kamal, Noor Azmi Shaharuddin, Khairul Basyar Baharudin, Norliza Abu Bakar
    MyJurnal
    Water contamination by herbicides and chelating agents is increasing mainly due to the
    increasing agricultural activities. Water contamination by these compounds has become a
    concern due to their adverse effects to the environment and humans. Seven sampling sites of
    water sources in Selangor and Johor were chosen for the study. Contamination level of
    Mecoprop (MCCP), Nitrilotriacetic acid (NTA) and Ethylenediaminetetraacetic acid (EDTA) in
    these water body areas was determined by using Gas Chromatography-Electron Capture
    Detector (GC-ECD). Our results indicated that water samples of Sungai Melot in Selangor
    showed the highest presence of EDTA. MCCP was detected at a high level at Sungai Sarang
    Buaya, Johor while NTA showed similar level of concentration at three different sites, Ladang
    10, Ladang Sayur and Mardi, Selangor.
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