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  1. Fulltext A New Method of Rice Moisture Content Determination Using Voxel Weighting-Based from Radio Tomography Images
    Mohd Ramli NA, Fazalul Rahiman MH, Kamarudin LM, Mohamed L, Zakaria A, Ahmad A, et al.
    Sensors (Basel), 2021 May 26;21(11).
    PMID: 34073162 DOI: 10.3390/s21113686
    This manuscript presents a new method to monitor and localize the moisture distribution in a rice silo based on tomography images. Because the rice grain is naturally hygroscopic, the stored grains' quality depends on their level of moisture content. Higher moisture content leads to fibre degradation, making the grains too frail and possibly milled. If the moisture is too low, the grains become brittle and are susceptible to higher breakage. At present, the single-point measurement method is unreliable because the moisture build-up inside the silo might be distributed unevenly. In addition, this method mostly applies gravimetric analysis, which is destructive. Thus, we proposed a radio tomographic imaging (RTI) system to address these problems. Four simulated phantom profiles at different percentages of moisture content were reconstructed using Newton's One-Step Error Reconstruction and Tikhonov Regularization algorithms. This simulation study utilized the relationship between the maximum voxel weighting of the reconstructed RTI image and the percentage of moisture content. The outcomes demonstrated promising results, in which the weighting voxel linearly increased with the percentage of moisture content, with a correlation coefficient higher than 0.95 was obtained. Therefore, the results support the possibility of using the RTI approach for monitoring and localizing the moisture distribution inside the rice silo.
  2. A Review of Gene Knockout Strategies for Microbial Cells
    Tang PW, Chua PS, Chong SK, Mohamad MS, Choon YW, Deris S, et al.
    Recent Pat Biotechnol, 2015;9(3):176-97.
    PMID: 27185502
    BACKGROUND: Predicting the effects of genetic modification is difficult due to the complexity of metabolic net- works. Various gene knockout strategies have been utilised to deactivate specific genes in order to determine the effects of these genes on the function of microbes. Deactivation of genes can lead to deletion of certain proteins and functions. Through these strategies, the associated function of a deleted gene can be identified from the metabolic networks.

    METHODS: The main aim of this paper is to review the available techniques in gene knockout strategies for microbial cells. The review is done in terms of their methodology, recent applications in microbial cells. In addition, the advantages and disadvantages of the techniques are compared and discuss and the related patents are also listed as well.

    RESULTS: Traditionally, gene knockout is done through wet lab (in vivo) techniques, which were conducted through laboratory experiments. However, these techniques are costly and time consuming. Hence, various dry lab (in silico) techniques, where are conducted using computational approaches, have been developed to surmount these problem.

    CONCLUSION: The development of numerous techniques for gene knockout in microbial cells has brought many advancements in the study of gene functions. Based on the literatures, we found that the gene knockout strategies currently used are sensibly implemented with regard to their benefits.

  3. A finite element study: Finding the best configuration between unilateral, hybrid, and ilizarov in terms of biomechanical point of view
    Abd Aziz AU, Abdul Wahab AH, Abdul Rahim RA, Abdul Kadir MR, Ramlee MH
    Injury, 2020 Nov;51(11):2474-2478.
    PMID: 32798038 DOI: 10.1016/j.injury.2020.08.001
    In an open fracture, the external fixator is one of the definitive treatment options as it could provide the initial stabilisation of the fractured bone. Limited literature discussing on the biomechanical stability between unilateral, hybrid and Ilizarov configurations, principally in treating a femoral fracture. Thus, this study aims to analyse the biomechanical stability of different external fixators via the finite element method (FEM). The present study portrays that different configurations of fixators possess different biomechanical stability, hence leading to different healing rates and complication risks. For the methodology, three-dimensional models of three different external fixators were reconstructed where axial loads were applied on the proximal end of the femur, simulating the stance phase. From the results, the unilateral configuration provides better stability compared to the hybrid and Ilizarov, where it displaced the least with an average percentage difference of 50% for the fixator's frame and 23% for the bone. The unilateral configuration also produced the least interfragmentary movement (0.48 mm) as compared to hybrid (0.62 mm) and Ilizarov (0.61 mm) configurations. Besides, the strain and stress of the unilateral configuration were superior in terms of stability compared to the other two configurations. As a conclusion, the unilateral configuration had the best biomechanical stability as it was able to assist the bone healing process as well as minimising the risk of pin tract infection while treating a femoral fracture.
  4. A rapid colorimetric screening method for vanillic acid and vanillin-producing bacterial strains
    Zamzuri NA, Abd-Aziz S, Rahim RA, Phang LY, Alitheen NB, Maeda T
    J Appl Microbiol, 2014 Apr;116(4):903-10.
    PMID: 24314059 DOI: 10.1111/jam.12410
    To isolate a bacterial strain capable of biotransforming ferulic acid, a major component of lignin, into vanillin and vanillic acid by a rapid colorimetric screening method.
  5. Fulltext A refined medium to enhance the antimicrobial activity of postbiotic produced by Lactiplantibacillus plantarum RS5
    Ooi MF, Foo HL, Loh TC, Mohamad R, Rahim RA, Ariff A
    Sci Rep, 2021 Apr 07;11(1):7617.
    PMID: 33828119 DOI: 10.1038/s41598-021-87081-6
    Postbiotic RS5, produced by Lactiplantibacillus plantarum RS5, has been identified as a promising alternative feed supplement for various livestock. This study aimed to lower the production cost by enhancing the antimicrobial activity of the postbiotic RS5 by improving the culture density of L. plantarum RS5 and reducing the cost of growth medium. A combination of conventional and statistical-based approaches (Fractional Factorial Design and Central Composite Design of Response Surface Methodology) was employed to develop a refined medium for the enhancement of the antimicrobial activity of postbiotic RS5. A refined medium containing 20 g/L of glucose, 27.84 g/L of yeast extract, 5.75 g/L of sodium acetate, 1.12 g/L of Tween 80 and 0.05 g/L of manganese sulphate enhanced the antimicrobial activity of postbiotic RS5 by 108%. The cost of the production medium was reduced by 85% as compared to the commercially available de Man, Rogosa and Sharpe medium that is typically used for Lactobacillus cultivation. Hence, the refined medium has made the postbiotic RS5 more feasible and cost-effective to be adopted as a feed supplement for various livestock industries.
  6. Fulltext A review on Lactococcus lactis: from food to factory
    Song AA, In LLA, Lim SHE, Rahim RA
    Microb Cell Fact, 2017 04 04;16(1):55.
    PMID: 28376880 DOI: 10.1186/s12934-017-0669-x
    Lactococcus lactis has progressed a long way since its discovery and initial use in dairy product fermentation, to its present biotechnological applications in genetic engineering for the production of various recombinant proteins and metabolites that transcends the heterologous species barrier. Key desirable features of this gram-positive lactic acid non-colonizing gut bacteria include its generally recognized as safe (GRAS) status, probiotic properties, the absence of inclusion bodies and endotoxins, surface display and extracellular secretion technology, and a diverse selection of cloning and inducible expression vectors. This have made L. lactis a desirable and promising host on par with other well established model bacterial or yeast systems such as Escherichia coli, Saccharomyces [corrected] cerevisiae and Bacillus subtilis. In this article, we review recent technological advancements, challenges, future prospects and current diversified examples on the use of L. lactis as a microbial cell factory. Additionally, we will also highlight latest medical-based applications involving whole-cell L. lactis as a live delivery vector for the administration of therapeutics against both communicable and non-communicable diseases.
  7. An Optical Tomography System Using a Digital Signal Processor
    Rahim RA, Thiam CK, Rahiman MH
    Sensors (Basel), 2008 Mar 27;8(4):2082-2103.
    PMID: 27879811
    The use of a personal computer together with a Data Acquisition System (DAQ) as the processing tool in optical tomography systems has been the norm ever since the beginning of process tomography. However, advancements in silicon fabrication technology allow nowadays the fabrication of powerful Digital Signal Processors (DSP) at a reasonable cost. This allows this technology to be used in an optical tomography system since data acquisition and processing can be performed within the DSP. Thus, the dependency on a personal computer and a DAQ to sample and process the external signals can be reduced or even eliminated. The DSP system was customized to control the data acquisition process of 16x16 optical sensor array, arranged in parallel beam projection. The data collected was used to reconstruct the cross sectional image of the pipeline conveyor. For image display purposes, the reconstructed image was sent to a personal computer via serial communication. This allows the use of a laptop to display the tomogram image besides performing any other offline analysis.
  8. An effective extracellular protein secretion by an ABC transporter system in Escherichia coli: statistical modeling and optimization of cyclodextrin glucanotransferase secretory production
    Low KO, Mahadi NM, Rahim RA, Rabu A, Abu Bakar FD, Murad AM, et al.
    J Ind Microbiol Biotechnol, 2011 Sep;38(9):1587-97.
    PMID: 21336875 DOI: 10.1007/s10295-011-0949-0
    Direct transport of recombinant protein from cytosol to extracellular medium offers great advantages, such as high specific activity and a simple purification step. This work presents an investigation on the potential of an ABC (ATP-binding cassette) transporter system, the hemolysin transport system, for efficient protein secretion in Escherichia coli (E. coli). A higher secretory production of recombinant cyclodextrin glucanotransferase (CGTase) was achieved by a new plasmid design and subsequently by optimization of culture conditions via central composite design. An improvement of at least fourfold extracellular recombinant CGTase was obtained using the new plasmid design. The optimization process consisted of 20 experiments involving six star points and six replicates at the central point. The predicted optimum culture conditions for maximum recombinant CGTase secretion were found to be 25.76 μM IPTG, 1.0% (w/v) arabinose and 34.7°C post-induction temperature, with a predicted extracellular CGTase activity of 68.76 U/ml. Validation of the model gave an extracellular CGTase activity of 69.15 ± 0.71 U/ml, resulting in a 3.45-fold increase compared to the initial conditions. This corresponded to an extracellular CGTase yield of about 0.58 mg/l. We showed that a synergistic balance of transported protein and secretory pathway is important for efficient protein transport. In addition, we also demonstrated the first successful removal of the C-terminal secretion signal from the transported fusion protein by thrombin proteolytic cleavage.
  9. Anti-breast cancer effects of live, heat-killed and cytoplasmic fractions of Enterococcus faecalis and Staphylococcus hominis isolated from human breast milk
    Hassan Z, Mustafa S, Rahim RA, Isa NM
    In Vitro Cell Dev Biol Anim, 2016 Mar;52(3):337-348.
    PMID: 26659392 DOI: 10.1007/s11626-015-9978-8
    Development of tumour that is resistant to chemotherapeutics and synthetic drugs, coupled with their life-threatening side effects and the adverse effects of surgery and hormone therapies, led to increased research on probiotics' anticancer potentials. The current study investigated the potential of live, heat-killed cells (HKC) and the cytoplasmic fractions (CF) of Enterococcus faecalis and Staphylococcus hominis as anti-breast cancer agents. MCF-7 cell line was treated with 25, 50, 100 and 200 μg/mL each of live, HKC and CF of the bacteria; and cytotoxicity was evaluated for 24, 48 and 72 h using MTT assay. The morphological features of the treated cells were examined by fluorescence microscopy. The stage of cell cycle arrest and apoptosis were quantified by flow cytometry. The bacterial effect on non-malignant breast epithelial cell line, MCF-10A, was assessed using MTT assay for 24, 48 and 72 h. All the three forms of the bacteria caused a significant decrease in MCF-7 (up to 33.29%) cell proliferation in concentration- and time-dependent manner. Morphological features of apoptosis like cell death, cell shrinkage and membrane blebbing were observed. Flow cytometry analyses suggested that about 34.60% of treated MCF-7 was undergoing apoptosis. A strong anti-proliferative activity was efficiently induced through sub-G1 accumulation (up to 83.17%) in treated MCF-7 and decreased number in the G0/G1 phase (74.39%). MCF-10A cells treated with both bacteria showed no significant difference with the untreated (>90% viability). These bacteria can be used as good alternative nutraceutical with promising therapeutic indexes for breast cancer because of their non-cytotoxic effects to normal cells.
  10. Association of social support and quality of life among people with schizophrenia receiving community psychiatric service: A cross-sectional study
    Munikanan T, Midin M, Daud TIM, Rahim RA, Bakar AKA, Jaafar NRN, et al.
    Compr Psychiatry, 2017 05;75:94-102.
    PMID: 28342379 DOI: 10.1016/j.comppsych.2017.02.009
    OBJECTIVE: To understand the needs of patients with schizophrenia for recovery, this study examined the type and level of social support and its association with quality of life (QOL) among this group of patients in the city of Kuala Lumpur.

    METHOD: A cross-sectional study was conducted on 160 individuals with schizophrenia receiving community psychiatric services in Hospital Kuala Lumpur (HKL). The WHOQOL-BREF, Brief Psychiatric Rating Scale (BPRS) and Multidimensional Scale of Perceived Social Support (MSPSS) were used to assess QOL, severity of symptoms and social support, respectively. The study respondents were predominantly Malay, aged less than 40, males, single, unmarried, had lower education levels and unemployed.

    RESULTS: About 72% of the respondents had poor perceived social support, with support from significant others being the lowest, followed by friends and family. From multiple regression analysis, social support (total, friend and family) significantly predicted better QOL in all domains; [B=0.315 (p<0.001), B=0.670 (p<0.001), B=0.257 (p<0.031)] respectively in Physical Domain; [B=0.491 (p<0.001), B=0.735 (p<0.001), B=0.631 (p<0.001)] in Psychological Domain; [B=1.065 (p<0.001), B=0.670 (p<0.017), B=2.076 (p<0.001)] in Social Domain and; [B=0.652 (p<0.001), B=1.199 (p<0.001), B=0.678 (p<0.001)] in Environmental Domain. Being married and having shorter duration of illness, lower BPRS (total) scores, female gender and smoking, were also found to significantly predict higher QOL.

    CONCLUSION: Social support is an important missing component among people with schizophrenia who are already receiving formal psychiatric services in Malaysia.

  11. Biomechanical analysis of three different types of fixators for anterior cruciate ligament reconstruction via finite element method: a patient-specific study
    Zainal Abidin NA, Abdul Wahab AH, Abdul Rahim RA, Abdul Kadir MR, Ramlee MH
    Med Biol Eng Comput, 2021 Sep;59(9):1945-1960.
    PMID: 34392448 DOI: 10.1007/s11517-021-02419-6
    Complication rates of anterior cruciate ligament reconstruction (ACL-R) were reported to be around 15% although it is a common arthroscopic procedure with good outcomes. Breakage and migration of fixators are still possible even months after surgery. A fixator with optimum stability can minimise those two complications. Factors that affect the stability of a fixator are its configuration, material, and design. Thus, this paper aims to analyse the biomechanical effects of different types of fixators (cross-pin, interference screw, and cortical button) towards the stability of the knee joint after ACL-R. In this study, finite element modelling and analyses of a knee joint attached with double semitendinosus graft and fixators were carried out. Mimics and 3-Matic softwares were used in the development of the knee joint models. Meanwhile, the graft and fixators were designed by using SolidWorks software. Once the meshes of all models were finished in 3-Matic, simulation of the configurations was done using MSC Marc Mentat software. A 100-N anterior tibial load was applied onto the tibia to simulate the anterior drawer test. Based on the findings, cross-pin was found to have optimum stability in terms of stress and strain at the femoral fixation site for better treatment of ACL-R.
  12. Fulltext Biosynthesis of ZnO Nanoparticles by a New Pichia kudriavzevii Yeast Strain and Evaluation of Their Antimicrobial and Antioxidant Activities
    Moghaddam AB, Moniri M, Azizi S, Rahim RA, Ariff AB, Saad WZ, et al.
    Molecules, 2017 May 24;22(6).
    PMID: 28538674 DOI: 10.3390/molecules22060872
    The potential ability of a new yeast strain, Pichia kudriavzevii, in the synthesis of zinc oxide nanoparticles (ZnO-NPs) through a green method was explored in this study. The effect of reaction time (12, 24 and 36 h) on the structure of the resulting ZnO nanoparticles was investigated. From the XRD and TEM results, the ZnO-NPs with a hexagonal wurtzite structure and a particle crystal size of ~10-61 nm was formed at different reaction times. Combing XRD, TEM, and PL results, it was revealed that the sample prepared at intermediate duration (24 h) has the most favorable nanosized structure with the lowest defect concentration. The biomedical properties of ZnO-NPs as free radical scavenging activity, cytotoxicity and antibacterial agents were characterized. Biosynthesized ZnO-NPs showed strong DPPH free radical scavenging and a dose dependent toxicity with non-toxic effects on Vero cells for concentrations below 190 µg/mL. Desirable bactericidal activity was shown by the ZnO-NPs on Gram-positive bacteria (Bacillus subtilis, Staphylococcus epidermidis and Staphylococcus aurous) and Gram-negative bacteria (Escherichia coli and Serratia marcescens). A maximum inhibition zone of ~19 mm was observed for Staphylococcus epidermidis at a concentration of 100 µg/mL for sample prepared at 24 h. The results from this study reveal that ZnO-NPs possesses potential for many medical and industrial applications.
  13. Biosynthesis of high molecular weight hyaluronic acid by Streptococcus zooepidemicus using oxygen vector and optimum impeller tip speed
    Lai ZW, Rahim RA, Ariff AB, Mohamad R
    J Biosci Bioeng, 2012 Sep;114(3):286-91.
    PMID: 22608992 DOI: 10.1016/j.jbiosc.2012.04.011
    The potential use of n-dodecane and n-hexadecane as oxygen vectors for enhancing hyaluronic acid (HA) biosynthesis by Streptococcus zooepidemicus ATCC 39920 was investigated using a 2-L stirred-tank bioreactor equipped with helical ribbon or Rushton turbine impellers. The volumetric fraction of the oxygen vector influenced the gas-liquid volumetric oxygen transfer coefficient (K(L)a) positively. Batch HA fermentation with 1% (v/v) n-dodecane or 0.5% (v/v) n-hexadecane addition was carried out at different impeller tip speeds. Even though cell growth was lower in the fermentation with oxygen vector addition, the HA productivity and molecular weight were higher when compared to the fermentation without oxygen vector at low impeller tip speed. The highest HA concentration (4.25 gHA/l) and molecular weight (1.54 × 10(7) Da) were obtained when 0.5% (v/v) n-hexadecane and 0.785 m/s impeller tip speed of helical ribbon were used.
  14. CD47 and CD36 expressions in the placenta of mothers with chorioamnionitis
    Hanim BS, Rahim RA, Mohd Salleh MF, Zakaria H, Abd Shukor N
    Malays J Pathol, 2023 Dec;45(3):463-471.
    PMID: 38155387
    INTRODUCTION: Chorioamnionitis is the inflammation of the placenta and is histologically defined as the presence of neutrophilic infiltration into the chorio-amnion membrane with and without involvement of the umbilical cord. Currently, the inflammatory mediators involved in the eliciting of inflammatory response is still largely under investigation. CD47 and CD36 are pro-inflammatory molecules that are still under investigation. The aim of this study was to determine the expressions of CD47 and CD36 in the placenta of mothers with chorioamnionitis.

    MATERIALS AND METHODS: This was a cross-sectional study, involving a total of 100 cases that comprised of acute subchorionitis (stage I, n=20), acute chorioamnionitis (stage II, n=20), acute necrotising chorioamnionitis (stage III, n=20) and non-chorioamnionitis placenta as control (n=40). All tissue blocks were retrieved from the archived pathology record over a period of 4 years. CD36 and CD47 immunohistochemistry were performed on all cases and their expression in various cell types on the placenta were analysed.

    RESULTS: CD36 was expressed only on the foetal vascular endothelial cells. Interestingly, CD47 showed positive staining on the neutrophils and its expression was significantly different between maternal inflammatory response stage II chorioamnionitis (n=13/20, p<0.001) with stage I and stage III chorioamnionitis.

    DISCUSSION: Our study showed CD47 was expressed in the neutrophils and it was associated with poorer perinatal outcomes and it may have a role in the pathogenesis of chorioamnionitis.

  15. Catharanthus roseus Aqueous Extract is Cytotoxic to Jurkat Leukaemic T-cells but Induces the Proliferation of Normal Peripheral Blood Mononuclear Cells
    Ahmad NH, Rahim RA, Mat I
    Trop Life Sci Res, 2010 Dec;21(2):101-13.
    PMID: 24575203
    Research on natural products has been widely used as a strategy to discover new drugs with potential for applications in complementary medicines because they have fewer side effects than conventional drugs. The aim of the present study was to evaluate the in vitro cytotoxic effects of crude aqueous Catharanthus roseus extract on Jurkat cells and normal peripheral blood mononuclear cells (PBMCs). The aqueous extract was standardised to vinblastine by high performance liquid chromatography (HPLC) and was used to determine cytotoxicity by the MTS [3-(4,5-dimethylthiazol-2-yl)-5(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay. DNA fragmentation assay was employed to determine if cell death was due to apoptosis. The results showed that the aqueous extract induced cell death of Jurkat cells at 24, 48 and 72 hours post-treatment in a time- and dose-dependent manner. However, cells treated at 48 and 72 hours produced higher cytotoxic effects with half maximal inhibitory concentration (IC50) values of 2.55 μg/ml and 2.38 μg/ml, respectively. In contrast, the extract induced normal PBMC proliferation, especially after 24 hours treatment with 1000 μg/ml. This result indicates that the C. roseus crude aqueous extract showed differential effects of inhibiting the proliferation of the Jurkat cell line and promoting the growth of PBMCs. These data suggest that the extract may be applicable for modulating the normal and transformed immune cells in leukaemia patients.
  16. Cell Wall-Treated Lactococcus lactis Increases the Plasmid Transfer Efficiency of Internal Ribosome Entry Site-Incorporated Lactococcal Bicistronic Vector into DF1 Cells
    Mat Isa N, Abdul Mutalib NE, Alitheen NB, Song AA, Rahim RA
    J. Mol. Microbiol. Biotechnol., 2017;27(4):246-251.
    PMID: 29055951 DOI: 10.1159/000481257
    This study demonstrates that cell wall treatment of Lactococcus lactis harbouring the internal ribosome entry site-incorporated lactococcal bicistronic vector pNZ:VIG mediated the delivery of genes into an eukaryotic cell line, DF1 cells, through bactofection. Bactofection analysis showed that the pNZ:VIG plasmid in L. lactis can be transferred into DF1 cells and that both the VP2 and gfp genes cloned in the plasmid can be transcribed and translated. The protein band relative to the Mr of VP2 protein (49 kDa) was successfully detected via Western blot analysis, while green fluorescence was successfully detected using a fluorescence microscope. The intensity of the bands detected increased for samples treated with both 1.5% (w/v) glycine and 10 μg/mL of lysozyme when compared to L. lactis treated with glycine alone and without treatment. Cell wall treatment of L. lactis with a combination of both glycine and lysozyme was not only shown to mediate plasmid transfer to DF1 cells, but also to increase the plasmid transfer efficiency.
  17. Fulltext Characterization of Gold-Sputtered Zinc Oxide Nanorods-a Potential Hybrid Material
    Perumal V, Hashim U, Gopinath SC, Rajintra Prasad H, Wei-Wen L, Balakrishnan SR, et al.
    Nanoscale Res Lett, 2016 Dec;11(1):31.
    PMID: 26787050 DOI: 10.1186/s11671-016-1245-8
    Generation of hybrid nanostructures has been attested as a promising approach to develop high-performance sensing substrates. Herein, hybrid zinc oxide (ZnO) nanorod dopants with different gold (Au) thicknesses were grown on silicon wafer and studied for their impact on physical, optical and electrical characteristics. Structural patterns displayed that ZnO crystal lattice is in preferred c-axis orientation and proved the higher purities. Observations under field emission scanning electron microscopy revealed the coverage of ZnO nanorods by Au-spots having diameters in the average ranges of 5-10 nm, as determined under transmission electron microscopy. Impedance spectroscopic analysis of Au-sputtered ZnO nanorods was carried out in the frequency range of 1 to 100 MHz with applied AC amplitude of 1 V RMS. The obtained results showed significant changes in the electrical properties (conductance and dielectric constant) with nanostructures. A clear demonstration with 30-nm thickness of Au-sputtering was apparent to be ideal for downstream applications, due to the lowest variation in resistance value of grain boundary, which has dynamic and superior characteristics.
  18. Characterization of pR18, a novel rolling-circle replication plasmid from Lactobacillus plantarum
    Jalilsood T, Baradaran A, Ling FH, Mustafa S, Yusof K, Rahim RA
    Plasmid, 2014 May;73:1-9.
    PMID: 24785193 DOI: 10.1016/j.plasmid.2014.04.004
    Lactobacillus plantarum PA18, a strain originally isolated from the leaves of Pandanus amaryllifolius, contains a pR18 plasmid. The pR18 plasmid is a 3211bp circular molecule with a G+C content of 35.8%. Nucleotide sequence analysis revealed two putative open reading frames, ORF1 and ORF2, in which ORF2 was predicted (317 amino acids) to be a replication protein and shared 99% similarity with the Rep proteins of pLR1, pLD1, pC30il, and pLP2000, which belong to the RCR pC194/pUB110 family. Sequence analysis also indicated that ORF1 was predicted to encode linA, an enzyme that enzymatically inactivates lincomycin. The result of Southern hybridization and mung bean nuclease treatment confirmed that pR18 replicated via the RCR mechanism. Phylogenetic tree analysis of pR18 plasmid proteins suggested that horizontal transfer of antibiotic resistance determinants without genes encoding mobilization has not only occurred between Bacillus and Lactobacillus but also between unrelated bacteria. Understanding this type of transfer could possibly play a key role in facilitating the study of the origin and evolution of lactobacillus plasmids. Quantitative PCR showed that the relative copy number of pR18 was approximately 39 copies per chromosome equivalent.
  19. Characterization of vibrio parahaemolyticus isolated from coastal seawater in peninsular Malaysia
    Tanil GB, Radu S, Nishibuchi M, Rahim RA, Napis S, Maurice L, et al.
    Southeast Asian J. Trop. Med. Public Health, 2005 Jul;36(4):940-5.
    PMID: 16295549
    Twenty-one Vibrio parahaemolyticus isolates representing 21 samples of coastal seawater from three beaches in peninsular Malaysia were found to be sensitive to streptomycin, norfloxacin and chloramphenicol. Resistance was observed to penicillin (100%), ampicillin (95.2%), carbenicilin (95.2%), erythromycin (95.2%), bacitracin (71.4%), cephalothin (28.6%), moxalactam (28.6%), kanamycin (19.1%), tetracycline (14.3%), nalidixic acid (9.5%) and gentamicin (9.5%). Plasmids of 2.6 to 35.8 mDa were detected among plasmid-containing isolates. All isolates carried the Vp-toxR gene specific to V. parahaemolyticus and were negative for the tdh gene, but only one isolate was positive for the trh gene. DNA fingerprinting of the isolates using ERIC-PCR and PFGE showed that the isolates belong to two major clonal groups, with several isolates from different locations in the same group, indicating the presence of similar strains in the different locations.
  20. Cloning and in silico characterization of two signal peptides from Pediococcus pentosaceus and their function for the secretion of heterologous protein in Lactococcus lactis
    Baradaran A, Sieo CC, Foo HL, Illias RM, Yusoff K, Rahim RA
    Biotechnol Lett, 2013 Feb;35(2):233-8.
    PMID: 23076361 DOI: 10.1007/s10529-012-1059-4
    Fifty signal peptides of Pediococcus pentosaceus were characterized by in silico analysis and, based on the physicochemical analysis, (two potential signal peptides Spk1 and Spk3 were identified). The coding sequences of SP were amplified and fused to the gene coding for green fluorescent protein (GFP) and cloned into Lactococcus lactis pNZ8048 and pMG36e vectors, respectively. Western blot analysis indicated that the GFP proteins were secreted using both heterologous SPs. ELISA showed that the secretion efficiency of GFP using Spk1 (0.64 μg/ml) was similar to using Usp45 (0.62 μg/ml) and Spk3 (0.58 μg/ml).
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