Malaysian Journal of Biochemistry
& Molecular Biology
(E-ISSN: 2600-9005)
The Official Publication of the Malaysian Society for Biochemistry & Molecular Biology (MSBMB)
Indexed by SCOPUS and Malaysian Citation Index (MYCITE)
ANNOUNCEMENT
With effect from 15th January 2023, all new submissions will be subjected to a MYR250 publication fee for every accepted paper.
CURRENT ISSUE & SPECIAL ISSUE
December 2023
Malay. J. Biochem. Mol. Biol. (2023) 26 (2)
TABLE OF CONTENTS
Page 1- 5
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Aisyah Mohd Ismail, Wan Rozianoor Mohd Hassan, Abd Razzif Abd Razak and Farida Zuraina Mohd Yusof
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GENETIC TYPING OF THREE MALAYSIAN DURIAN VARIETIES USING SIMPLE SEQUENCE REPEAT (SSR) MARKERS
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Abstract
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There have been few studies on the molecular aspects of durian up to this point. Although morphological classification is practical, simple, and quick, it suffers from phenotypic plasticity due to environmental influences and age. Hence, the genetic characterization of durian varieties needs to be carried out. This study was performed to evaluate the effectiveness of three simple sequence repeat (SSR) markers to identify and discriminate three durian types: MK (Musang King), D24 and D101. Successful amplification of SSR regions were observed in the durian DNA samples. A total of 8 alleles were generated by all primers. Both DZ01 and DZ04 primers showed the highest number of polymorphic fragments. Among the three SSR primers, DZ03 is the least informative with only 2 number of alleles produced. The most important finding of this study was that each primer is unique and specific to one type of durian sample. This preliminary study showed that the SSR loci could be used as genetic markers to assist future durian breeding program.
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Page 6 - 30
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Hui Shi Saw, Bernard Kok Bang Lee, Hwei-San Loh
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GENE EXPRESSION MINING AND in silico ANALYSIS OF DIFFERENTIALLY EXPRESSED GENES IN HEAD AND NECK CANCER
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Abstract
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The advancement of high-throughput transcriptome profiling techniques, such as next-generation sequencing and microarray, has led to the development of bioinformatics tools and databases for functional genomics. Integrated bioinformatics analysis has emerged as a promising strategy to address the major cause of morbidity and death globally: cancer. In this study, we aimed to use an integrated bioinformatics pipeline to identify potential molecular biomarkers for diagnosis and prognosis in cancer studies. Specifically, we focused on head and neck squamous cell carcinoma (HNSCC). To achieve this, we performed a meta-analysis on expression datasets from the Gene Expression Omnibus (GEO) using GEO2R to derive differentially expressed genes (DEGs). Subsequently, we conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Protein-protein interaction networks of the up-regulated and down-regulated genes were constructed using the STRING database, and the top ten hub genes for each group were identified using cytoHubba. The relative mRNA expression of the identified DEGs was validated with GEPIA2, and their correlation with the overall survival of HNSCC patients was assessed using Kaplan-Meier analysis. Combining our findings with published evidence, we observed that the up-regulated genes primarily function in the extracellular matrix and cell cycle regulation. In contrast, the down-regulated genes are involved in muscle contraction. Our results suggest that six down-regulated genes (MYL1, MYL3, MYH6, MYLPF, ACTA1, TTN) and five up-regulated genes (CDC20, CCNB1, MAD2L1, TOP2A, MMP9) have the potential to serve as diagnosis biomarkers. In contrast, five up-regulated genes (FN1, CDK1, PLK1, AURKA, CD44) could be used for prognosis and diagnosis in the clinical analysis of HNSCC. This study demonstrated the effectiveness of an integrated bioinformatics approach in identifying clinically relevant biomarkers for HNSCC, and the pipeline could be applied to other cancer datasets. Further investigation of the identified biomarkers will enrich our understanding of their involvement in the molecular mechanism of carcinogenesis and provide potential therapeutic targets for HNSCC.
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Page 31 - 38
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Yusnaini Md Yusoff, Ahmad Firdhaus Arham, Noor Sharizad Rusly, Muhammad Firdaus Aziz, Mohd Rosly Shaari, Jasni Sabri, Shanmugavelu Sithambaram, Noordin Mohd Mustapha, Tan Sheau Wei, Nursyuhada Haron, Nurul Huda Mohd Zairi, Mohd Hakimi Mohd Kassim and Hazilawati Hamzah
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MODULATING THE BCL2 TO BAX RATIO: TURMERIC’S POTENTIAL IN LEUKAEMIA THERAPY
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Abstract
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Leukaemia ranks among the ten most prevalent types of cancer in Malaysia, exhibiting a death rate of 4.4%. Therefore, the objective of this study was to assess the preventative effects of a high dose of dried Curcuma longa (C. longa) rhizomes supplementation in rats with N-Methyl-N-Nitrosourea (MNU)-induced leukaemia. Two weeks were spent acclimatizing 64 mature male Sprague Dawley rats. At week 0, all rats were separated into A, B, C, and D groups. MNU was intraperitoneally given to Group C and D rats at 240 mg/kg. C. longa rhizomes were dried and given to Groups B and D rats at 5000 mg/kg. Group A rats were controls. The rats were killed in week 20. Blood samples were examined for the presence of leukaemic cells and underwent RNA extraction for quantitative real-time polymerase chain reaction (RT-PCR). By blast cell appearance, all rats in Group C had 100% leukaemia in the blood smear, while Group D had 88%. The ratio of Bcl-2 to Bax transcripts in blood was 3.3-fold (10.50±1.26) higher in Group C compared to the control rats (3.17±1.07), indicating high levels of anti-apoptotic cells caused by leukaemia. Interestingly, the ratio of Bcl-2 to Bax transcripts in Group D rats (3.58±0.82) was similar to the control rats. A quantitative RT-PCR experiment found that adding dried C. longa rhizome to a meal significantly reduced Bcl2 to Bax ratio in leukaemia rats, which significantly reduced the incidence of leukaemia.
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Page 39 - 44
Hao Ing Yeoh, Md Salzihan Md Salleh, Maya Mazuwin Yahya, Andee Dzulkarnaen Zakaria, Wan Mohd Nazri Wan Zainon, Ahmad Aizat Abdul Aziz
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GENETIC ASSOCIATION OF ABCB1 1236 C>T POLYMORPHISM ON MALAY TRIPLE NEGATIVE BREAST CANCER (TNBC) SUSCEPTIBILITY RISK
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Abstract
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Triple-negative breast cancer (TNBC) is characterized by the absence of estrogen receptors (ER), progesterone receptors (PR), and the lack of amplification of the human epidermal growth factor 2 (HER2) receptor. Adenosine triphosphate-binding cassette (ABC) subfamily B member 1 (ABCB1) serves as a drug efflux transporter, facilitating the translocation of various substrates (xenobiotics, toxins, carcinogens, etc.) across the membrane in an ATP-dependent manner. Genetic variations on ABCB1 may lead to reduced substrate specificity, stability, and gene expression, thereby influencing the efflux activity of the protein. These variations can ultimately impact an individual’s susceptibility to cancer. The present study aims to investigate the association of polymorphisms in ABCB1 (1236 C > T, 2677 G > T/A, and 3435 C > T) in modulating the individual susceptibility risk to TNBC. DNA was extracted from blood samples collected from 75 TNBC patients and 100 healthy controls. Genotyping was performed using the PCR-RFLP technique, and the resulting genotype patterns were categorized into homozygous wild type, heterozygous, and homozygous variants. The association between genotype and TNBC and clinicopathological variables was assessed using the independent χ2 test. The strength of the association was determined by calculating the odds ratio (OR) with a 95% confidence interval. Subsequently, linkage disequilibrium and haplotype association analyses were performed to evaluate the association of the ABCB1 haplotype with TNBC susceptibility. Overall, carriers of TT genotype and T allele of ABCB1 1236 C > T exhibited an increased OR of 2.750 (95% CI: 1.054–7.175) and 1.545 (95% CI: 1.001–2.385) for developing TNBC. Specifically, the ABCB1 1236 C > T variant is significantly associated with early age at diagnosis, advanced TNM staging, and the metaplastic/medullary subtype of carcinoma. Lastly, the haplotype 1236C/3435T/2677G was also associated with a reduced risk of TNBC. In summary, ABCB1 1236 C > T polymorphism was associated with an increased risk of TNBC susceptibility and correlated with early age diagnosis, high tumor staging, and the metaplastic/medullary subtype in TNBC patients. This suggests a potential predictive role in TNBC susceptibility and development for this polymorphism.
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Page 45 - 54
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Nik Ida Mardiana Nik-Pa, Mohamad Farhan Mohamad Sobri, Nurhasliza Zolkefli, Suraini Abd-Aziz, Mohamad Faizal Ibrahim, Noorjahan Banu Mohamed Alitheen, Norhayati Ramli
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DECIPHERING THE MOLECULAR LANDSCAPE: IN-SILICO ANALYSIS OF CYCLODEXTRIN GLYCOSYLTRANSFERASE FOR ENHANCED ENZYME FUNCTIONALITY AND CYCLODEXTRIN SYNTHESIS
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Abstract
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Cyclodextrin glycosyltransferase (CGTase) has always played a significant role in the production of cyclodextrin through the cyclization reaction. The wide application of this valuable protein demands a better understanding, leading to a comprehensive in-silico analysis of CGTase. The analysis focused on the functional domain composition of the recombinant CGT-BS protein by comparing it with several other CGTase proteins from different Bacillus spp. A three-dimensional (3-D) model was constructed to predict the active, substrate binding and cyclization sites of the CGT-BS protein. Structural function prediction revealed the active site within domain A at the wide end of the (β/α)8-barrel, with Asp 268, Glu 296 and Asp 357 as the catalytic residues. Additionally, the reaction site for cyclization was identified in domain B at Tyr 234. In comparison to maltose binding sites (MBS) 1 and 2 which are associated with raw starch binding activity, a comparable role is deduced for the MBS identified on the surface of the Domain E protein. We additionally observed that the residues Tyr 139, Arg 266 and Asp 367, located at the substrate binding cleft of the catalytic site, exhibited heightened hydrophobicity and concurrent cyclization activity. The successful extracellular expression of the CGT-BS protein is also anticipated to be facilitated by the presence of a functional signal peptide. In conclusion, our in-depth in-silico analysis unveils critical insights into the structural and functional aspects of CGT-BS protein, laying the groundwork for further exploration of its catalytic mechanisms and potential applications in cyclodextrin synthesis.
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Page 55 - 65
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Gayathiri Verasoundarapandian, Chiew Yen Wong, Zheng Syuen Lim, Khadijah Nabilah Mohd Zahri, Syazani Darham, Nur Nadhirah Zakaria and Siti Aqlima Ahmad
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OPTIMISATION OF ANTARCTIC FILAMENTOUS ALGA GROWTH IN THE PRESENCE OF MOLYBDENUM
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Abstract
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Elevated concentrations of heavy metals have been identified in Antarctica due to growing anthropogenic activities in recent years. Molybdenum (Mo) is a trace element that has not been extensively studied in terms of its toxicity towards the environment, especially in extremely cold weather. The algae communities in the Antarctic were less focused and explored, unlike indigenous bacteria consortia in their response to heavy metals. The study aims to optimise the physicochemical conditions for optimal growth of an Antarctic algal, Klebsormidium sp. in the presence of Mo via conventional one‒factor‒at‒a‒time (OFAT) and growth kinetics analysis. Algal cultures with aeration showed a higher growth rate (μ = 0.2352 d-1) than those without aeration (μ = 0.1976 d-1). Based on the optimised parameter, the overall biomass yields with and without aeration systems correspond to each other (P > 0.05). It was discovered that the Klebsormidium sp. showed maximal growth in terms of biomass at 20 g/L of sucrose, 2 g/L of ammonium nitrate, 4 g/L NaCl concentration and pH 7.5. The overall optimised conditions were further analysed using the Exponential growth model, which demonstrated no significant difference (P > 0.05) in the algae growth rate with aeration (0.020 ± 0.0018 h-1) and without aeration (0.020 ± 0.0015 h-1). The Antarctic filamentous algae exhibited the ability to grow in heavy metal, Mo at optimal growth conditions, but the aeration systems did not affect the algae growth significantly. Therefore, this study could help in understanding the capability of algae to grow in the presence of heavy metal through various manipulations of growth parameters and act as a preliminary study for bioremediation of Mo in Antarctic polluted sites.
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Page 66 - 75
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Jye Ping Fam, Suriana Sabri, Syarul Nataqain Baharum, Lorrine Eseoghene Okojie, Siti Nur Hazwani Oslan,
Abu Bakar Salleh, Siti Nurbaya Oslan
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FATTY ACID AS THE POTENTIAL INDUCER FOR RECOMBINANT LIPASE EXPRESSION IN Meyerozyma guilliermondii STRAIN SO
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Abstract
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High amount of methanol concentration in the cultivation medium during the production of enzymes in methylotrophic yeast could inhibit the cell growth, level of enzyme expressed as well as limit the use of the enzyme for certain foods and pharmaceutical production. A recombinant T1 lipase was expressed using Meyerozyma guilliermondii strain SO as a host under the regulation of alcohol oxidase promoter without methanol induction. Thus, this study aimed to decipher an alternate innate inducer of the expression host by determining the metabolites present in the recombinant strain SO and investigate the expression of the bacterial lipase using the significant selected metabolite (fatty acids). The media from M. guilliermondii strain SO (wild type) and SO2 (recombinant strain) (at 0 and 60 h) were extracted using methanol extraction protocols followed by gas chromatography-mass spectrometry (GC-MS). A multivariate statistical analysis; principle component analysis (PCA) and partial least square discriminant analysis (PLSDA) were implemented to determine the relationship between the metabolites present in strain SO and SO2. The results showed that the primary metabolites; amino acids, organic acids and particularly, copious amounts of fatty acids, were significantly present in strain SO2 compared to strain SO. Further analysis of the identified fatty acids was conducted and the results showed that hexadecanoic acid (C16) showed an increase of 1.45 fold of T1 lipase expression in SO2 compared to the control experiment. This finding suggested that the fatty acid could be used as an alternative inducer for T1 lipase expression to reduce and/or eliminate the application of methanol.
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Page 76 - 85
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Nor Azlan Nor Muhammad, Chong Sheng Cheah, Nor Syafinaz Yaakob
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IN SILICO CHARACTERISATION OF A Polygonum minus SEQUENCE AS PUTATIVE BEACH DOMAIN PROTEIN
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Abstract
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Polygonum minus has been widely studied due to its significant content of flavonoid, phenolic and terpenoid compounds which are well-associated with medicinal properties. However, most of the pathways that regulate the development and synthesis of secondary metabolites of P. minus remained unknown. Identifying candidate genes and proteins that are involved in the biosynthetic pathways would contribute to a better understanding of the bioactive compound synthesis of P. minus. This study analysed and characterised a large 2151 amino acid hypothetical protein in P. minus using bioinformatic tools and databases. Sequence homology search, conserved domain prediction, protein hierarchical clustering, structure prediction and sub-cellular localisation prediction were done. Results from sequence homology search showed that it is a BEACH domain-containing protein. Analysis of its conserved domain revealed the presence of Concanavalin A-like lectin domain (ConA), Pleckstrin homology-like domain (PH), BEACH domain and WD40 domain repeats. Hierarchical clustering of protein supported that it has a close relationship with BEACH protein family members. The structure of the hypothetical protein was proposed and revealed the presence of a small pocket that functions for the binding of dsRNA. Sub-cellular localisation analysis suggested that the hypothetical protein is localized in the endoplasmic reticulum. It is proposed that the hypothetical protein is involved in the autophagy process in P. minus. This study serves as one of the keys to understanding the role of the hypothetical protein in the plant autophagy process which is important in immunity defence and stress tolerance of P. minus. Manipulation of the autophagy process may result in a better yield of secondary metabolites and promote the survival rate of P. minus.
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SPECIAL ISSUE (1) 2023
1st International Biotechnology, Microbiology and Environment Collaborative Sciences (BioMECs) Symposium
Guest Editor: Assoc. Prof. Ts. Dr. Nor'aishah Hasan, UiTM Cawangan Negeri Sembilan, Kampus Kuala Pilah, Negeri Sembilan
TABLE OF CONTENTS
Page 1- 7
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Dayang Hanim Alysha Abang Hamdani, Ilyanie Hj Yaacob, Ida Muryany Md Yasin
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SCREENING OF POTENTIAL PROBIOTIC CHARACTERISTICS OF LACTIC ACID BACTERIA ISOLATED FROM MALAYSIAN FERMENTED PEKASAM
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Abstract
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Lactic acid bacteria (LAB) from fermented foods are proven to be able to hinder the growth and activities of some foodborne pathogens. Antagonistic effects and sensitivity to antibiotics are important factors that need to be considered during the screening of potential probiotic strains. This study aims to evaluate the in vitro antagonistic activities with hemolytic activity and antibiotic susceptibility of LAB isolated from Malaysian fermented food, Pekasam Senek. Twenty LAB isolates were assessed for their antagonistic activities against Bacillus cereus, Escherichia coli, Klebsiella pneumoniae, and Shigella sonnei via the spot overlay method. LAB isolates with positive results in antagonistic proceeded with subsequent assay, hemolytic assay, and antibiotic susceptibility test. Bacterial cultures were streaked on a fresh blood agar plate to examine the signs of β-hemolysis, α-hemolysis, and γ-hemolysis. The antibiotic susceptibility patterns of the strains to six types of antibiotics were assessed through the disc diffusion method. Antagonistic evaluation tests showed that all LAB isolates were able to inhibit the growth of pathogenic bacteria with the highest inhibition zone (31 mm) produced by PS26 against E. coli. Twelve (12) isolates showed negative hemolytic activity which indicates that they are safe and screened out for their antibiotic susceptibility testing. Furthermore, all twelve isolates were susceptible to ampicillin, bacitracin, chloramphenicol, and erythromycin while resistant to streptomycin. This study indicates that LAB isolated from Pekasam Senek had significant antagonism ability against the tested pathogens with negative hemolysis. Meanwhile, the resistance patterns of the isolates varied depending on the different types of antibiotics.
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Page 8 - 15
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Ida Muryany M.Y., Chin Y.K., Ina-Salwany M.Y.
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RAPID IDENTIFICATION AND CHARACTERIZATION OF THE Lactobacillus STRAINS BY USING 16S-23S rRNA GENE INTERGENIC SPACER REGION AND recA GENES
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Abstract
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Lactic acid bacteria are known as potential probiotics that contribute beneficial effects for human beings and farmed animals. Identification of potential Lactic acid bacteria isolates was important for potential probiotic characterization. The isolates were under microscopic determination by Gram staining and electron screening microscopy to determine the morphology of the isolate, followed by rapid identification by using PCR amplification with ITS and recA genes to identify bacteria species of the isolates. Isolates L8 and L20 showed rod-shaped cells in the cluster while isolate S1 showed coccobacillus-shaped cells after the microscopic observation. L8 and L20 both isolates were identified as Lactobacillus plantarum while isolate S1 was identified as Lactobacillus pentosus after PCR amplification with ITS and recA genes. Our present experiment shows that ITS and recA genes can be used with PCR amplification to identify probiotic, Lactobacillus spp accurately.
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Page 16 - 22
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Ilyanie H.Y., Ida Muryany M.Y. and Huda-Faujan N.
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OPTIMIZED SAMPLE PREPARATION TECHNIQUE FOR VISUALISATION OF THE ADHERENCE OF LACTOBACILLACEAE SP. TO HUMAN COLORECTAL ADENOCARCINOMA CELL LINE HT-29 BY FIELD EMISSION SCANNING ELECTRON MICROSCOPE
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Abstract
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The objective of this study was to compare and determine the optimal sample preparation techniques to observe the adherence of probiotic bacteria, Lactobacillaceae sp. to human colorectal adenocarcinoma cell line HT-29. Different fixation times and coating thicknesses were compared to evaluate the integrity and quality of the image observed using a field emission scanning electron microscope (FESEM). Based on the qualitative assessments, the one-hour fixation was proposed as a promising fixation period as it is better than overnight fixation in terms of showing clearer parts and adhesive features on the surface of both bacteria and HT-29 cells. The platinum sputter-coating step is recommended at a shorter time to increase the conductivity of the sample and reduce electron beam damage. A thicker platinum coat could obscure fine structural visualization although it helps in eliminating charging during the imaging process. This finding provides an important sample preparation optimization to enable better structural integrity and quality of images captured using FESEM.
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Page 34 - 41
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Page 42 - 49
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Page 50 - 54
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Page 55 - 62
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Page 63 - 67
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Yasmin Ezzaty Abdul Shukur, Ina-Salwany Md Yasin and Aslizah Mohd-Aris
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DETECTION AND SEQUENCE ANALYSIS OF SIDEROPHORE BIOSYNTHETIC GENE PvsD FROM Vibrio harveyi VH1
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Abstract
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Numerous studies have been conducted to investigate siderophore genes in Vibrio species. There are many researches that have been done to learn about the siderophore genes in Vibrio species. Therefore, it is crucial to search the siderophore virulence-associated gene in the opportunistic pathogen from Vibrio harveyi, to predict the potential genes contribution to its pathogenicity. This study attempts to characterize the siderophore-associated gene from V. harveyi. The objectives are to identify and amplify the siderophore-associated gene from V. harveyi and to characterize the gene, based on molecular characterization and bioinformatic analysis. The results showed that the siderophore-associated gene from V. harveyi VH1 belongs to a part of Vibrioferrin gene cluster, which is the biosynthetic of the PvsD gene. In conclusion, the siderophores produced by V. harveyi VH1 belong to the vibrioferrin siderophores gene, which is responsible for helping this species accumulate iron from the environment.
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Page 23 - 33
Nabihah Raihanah Tajul Anuar, Roslina Ainna Roslan, Lyena Watty Zuraine Ahmad, Roziah Kambol, Sharifah Aminah Syed Mohamad, Farizan Aris, Nurul Aili Zakaria and Norfatimah Mohamed Yunus
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MOLECULAR DETECTION AND ANALYSIS OF BACTERIAL PANICLE BLIGHT PATHOGENS IN RICE FIELD IN MALAYSIA
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Abstract
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Bacterial panicle blight (BPB) disease is one of the major diseases of rice worldwide. Rapid detection of pathogens is compulsory to lead up to the discovery of effective control methods and resistant cultivars. In Malaysia, BPB was first detected in Sungai Ache, Pahang, Malaysia before it spread throughout Peninsular Malaysia. BPB has been estimated to affect up to 50% of the rice population. This study aims to identify the pathogens associated with BPB disease that infected rice fields in Peninsular Malaysia through molecular technique, without the culturing procedure, in order to propose a rapid and effective isolation method for pathogen detection from infected rice seeds. The seed samples, which exhibited BPB symptoms and without symptoms, were collected from five populations of rice fields in Sungai Burong, Selangor, Malaysia. The isolated DNA was characterized molecularly using polymerase chain reaction (PCR) and sequencing based on 16s rRNA. A total of 16 sequences were analyzed to find regions of local similarity between sequences through BLAST. Based on 16s rRNA phylogenetic analysis, 3 strains were clustered under the clade of Burkholderia glumae and another 3 were clustered with Pantoea agglomerans clade with bootstrap confidence value of 98 % and 100 %, respectively. Results from Data Analysis in Molecular Biology and Evolution (DAMBE) and Automatic Barcode Gap Discovery (ABGD) gave significant support and validate the phylogenetic analysis. A complete examination of bacterial genomic separation methods, as well as phylogenetic analysis of 16S marker for BPB pathogens would provide an effective and rapid tool for pathogens detection in crop biosecurity in the agricultural industry.
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Nur Ain Liana Rojnan and Nor Akmalazura Jani
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PHYTOCHEMICAL ANALYSIS AND DPPH RADICAL SCAVENGING ACTIVITY OF Plectranthus amboinicus (Lour.) Spreng LEAF EXTRACTS
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Abstract
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Plectranthus amboinicus (Lour.) Spreng (Lamiaceae) is traditionally used in folk medicine to treat countless illnesses. This study aimed to determine the phytochemical analysis including, phytochemical screening, total phenolic and flavonoid contents as well as DPPH radical scavenging activity of P. amboinicus leaf extracts. The extraction of phytochemicals was performed using sequential maceration method using n-hexane, ethyl acetate and methanol. Phytochemical screening was conducted using standard chemical tests, while total phenolic and flavonoid contents were performed using Folin-Ciocalteu and aluminum chloride colorimetric methods, respectively. All extracts were subjected to 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical assay. Preliminary phytochemical analysis revealed that the leaves of P. amboinicus consisted of flavonoids, phenols, terpenoids, glycosides and tannins, but showed negative results for alkaloids and saponins tests. The greatest phenolic content was observed in the ethyl acetate extract (73.31 ± 0.97 mg GAE/g), while the lowest value was reported in the n-hexane extract (24.63 ± 0.84 mg GAE/g). The ethyl acetate extract was also composed of the highest flavonoid content (95.72 ± 0.80 mg QE/g), while the methanol extract had the lowest flavonoid content (9.84 ± 0.69 mg QE/g). Among the extracts, the methanol extract demonstrated better DPPH radical scavenging activity with an IC50 of 878.37 μg/mL.
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Nurhamimah Zainal Abidin, Nur Fadiah Wathiqah Fadzillah and Muhammad Syakir Suhaimi
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ISOLATION AND IDENTIFICATION OF Bacillus cereus s.l. FROM VEGETABLES AND CEREALS FROM LOCAL MARKETS IN NEGERI SEMBILAN USING 16S rDNA AMPLICON SEQUENCING
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Abstract
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Bacillus cereus is a spore-forming food-borne pathogen that can cause food poisoning. The bacteria can produce toxins that lead to emetic and diarrheal intoxication. This study was designed to investigate the occurrence of B. cereus in different types of cereals and vegetables purchased from local markets in Negeri Sembilan using selective medium agar, biochemical approaches and bacterial species confirmation using 16S rDNA amplicon sequencing. A phylogenetic tree was then created using MEGA X software to identify the relationship between different bacterial species. From this study, the prevalence of B. cereus in cereal and vegetables was recorded at 38.5% and 9.1%, respectively. These suggest that the presence of B. cereus-containing cereals and vegetables in diets may represent the risk in the case of inadequate heat treatment.
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Siti Nur Nabeela A'ifah Mohammad, Salfarina Iberahim, Wan Suriana Wan Ab Rahman, Mohd Nazri Hassan, Hisham Atan Edinur, Maryam Azlan & Zefarina Zulkafli
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β-GLOBIN GENE CLUSTER MUTATION AND DELETION AMONG ANEMIC PATIENTS IN HOSPITAL UNIVERSITI SAINS MALAYSIA USING MULTIPLEX AMPLIFICATION REFRACTORY MUTATION SYSTEM POLYMERASE CHAIN REACTION (MARMS-PCR) AND GAP-PCR
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Abstract
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Anemia associated with high fetal hemoglobin (HbF) levels of more than 1.0%, can be impacted by several possible factors, including acquired and inherited causes. The aim of this study is to screen for β-globin gene cluster mutations among anaemic patients with high HbF (HbF >1%). The study involved 150 blood samples of anaemic patients from Hospital Universiti Sains Malaysia. High-performance liquid chromatography (HPLC) was performed on 150 anaemic samples to observe the levels of HbF and hemoglobin A2 (HbA2). One hundred six patients reported with high HbF levels (HbF >1%). The samples with HbA2 levels >3.2% were subjected to multiplex amplification refractory mutations system-polymerase chain reaction (MARMS-PCR), while those with HbA2 level ≤3.2% utilised gap-PCR. For MARMS-PCR, 61 out of 106 patients had the most frequent mutations detected in Cd 26 (35), followed by IVS1-5 (6), Cd 41/42 (3), Cd 8/9 (2) and IVS 1-1 (1). Furthermore, only one sample showed compound heterozygosity for Cd26 and Cd 8/9. However, for gap-PCR, there was no deletion detected in the 45 samples. This study shows the importance and significance of screening for high HbF levels and molecular characterisation in detecting various types of β-globin gene cluster mutations/deletions among anaemic patients for establishing a proper diagnosis and management.
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Umairah Ramli, Muhamad Arif Mohamad Jamali, Ismatul Nurul Asyikin Ismail, Fatin Hilyani Mohamad and
Liyana Azmi
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MOLECULAR DYNAMIC SIMULATIONS OF MlaC INHIBITION BY ANTIBIOTIC IN Escherichia coli
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Abstract
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Antimicrobial resistance has emerged as a global public health concern. Gram-negative bacteria such as Escherichia coli (E. coli) pose a significant threat to human health due to their increasing antibiotic resistance. For instance, Shiga toxin-producing E. coli (STEC) is a strain that produces toxins that cause damage to the lining of the intestines and kidneys. Antibiotic exposures to STEC would induce hemolytic uraemic syndrome and bloody diarrhoea, a potentially fatal condition to the patient. The outer membrane architecture in Gram-negatives, specifically the OmpC–Mla complex, maintains the outer membrane lipid asymmetry. The MlaC protein transfers phospholipids from outer membranes to inner membranes and ensures the integrity of the membrane. Inactivation of MlaC protein increases the penetrability of OM and increases the antibiotic’s sensitivity. Therefore, screening for inhibitor compounds that can bind and inhibit the function of MlaC is a viable strategy for antibiotic development. This study aims to understand the interactions of four types of inhibitors in MlaC protein from E. coli via docking and molecular dynamic (MD) simulation. The four types of inhibitors namely albacarcin V, clorobiocin, 1-N,4-N-bis(3-phenylphenyl)piperazine-1,4-dicarboxamide (piperazine dicarboxamide) and -2-[2-[(6-oxobenzo[c]chromen-2-yl)carbamoyl]phenyl]benzoic acid (salicylanilide benzoate). The docking showed that the inhibitors fit into the lipid pocket of MlaC. MD for each system run at 100 ns showed that the system has stable Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and reasonable Radius of Gyration (Rg) value. The RMSD, RMSF and Rg were comparable to the native phospholipid binding in the crystal structure, which suggests the potential use of these four types of inhibitors. Salicylanilide benzoate was revealed to be the most stable in complex with MlaC, with the least deviation, least fluctuation, and most compact throughout the simulation.
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