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.
Best viewed on desktop
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
​
Dayang Hanim Alysha Abang Hamdani, Ilyanie Hj Yaacob, Ida Muryany Md Yasin
​
SCREENING OF POTENTIAL PROBIOTIC CHARACTERISTICS OF LACTIC ACID BACTERIA ISOLATED FROM MALAYSIAN FERMENTED PEKASAM
​
Abstract
​
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.
​
​
​
Page 8 - 15
​
Ida Muryany M.Y., Chin Y.K., Ina-Salwany M.Y.
​
RAPID IDENTIFICATION AND CHARACTERIZATION OF THE Lactobacillus STRAINS BY USING 16S-23S rRNA GENE INTERGENIC SPACER REGION AND recA GENES
​
Abstract
​
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.
​
​
Page 16 - 22
​
Ilyanie H.Y., Ida Muryany M.Y. and Huda-Faujan N.
​
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
​
Abstract
​
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.
​
​
Page 34 - 41
​
Page 42 - 49
​
Page 50 - 54
​
Page 55 - 62
​
Page 63 - 67
​
Yasmin Ezzaty Abdul Shukur, Ina-Salwany Md Yasin and Aslizah Mohd-Aris
​
DETECTION AND SEQUENCE ANALYSIS OF SIDEROPHORE BIOSYNTHETIC GENE PvsD FROM Vibrio harveyi VH1
​
Abstract
​
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.
​
​
​
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
​
MOLECULAR DETECTION AND ANALYSIS OF BACTERIAL PANICLE BLIGHT PATHOGENS IN RICE FIELD IN MALAYSIA
​
Abstract
​
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.
​
​
Nur Ain Liana Rojnan and Nor Akmalazura Jani
​
PHYTOCHEMICAL ANALYSIS AND DPPH RADICAL SCAVENGING ACTIVITY OF Plectranthus amboinicus (Lour.) Spreng LEAF EXTRACTS
​
Abstract
​
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.
​
​
​
Nurhamimah Zainal Abidin, Nur Fadiah Wathiqah Fadzillah and Muhammad Syakir Suhaimi
​
ISOLATION AND IDENTIFICATION OF Bacillus cereus s.l. FROM VEGETABLES AND CEREALS FROM LOCAL MARKETS IN NEGERI SEMBILAN USING 16S rDNA AMPLICON SEQUENCING
​
Abstract
​
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.
​
​
​
Siti Nur Nabeela A'ifah Mohammad, Salfarina Iberahim, Wan Suriana Wan Ab Rahman, Mohd Nazri Hassan, Hisham Atan Edinur, Maryam Azlan & Zefarina Zulkafli
​
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
​
Abstract
​
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.
​
​
​
Umairah Ramli, Muhamad Arif Mohamad Jamali, Ismatul Nurul Asyikin Ismail, Fatin Hilyani Mohamad and
Liyana Azmi
​
MOLECULAR DYNAMIC SIMULATIONS OF MlaC INHIBITION BY ANTIBIOTIC IN Escherichia coli
​
Abstract
​
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.
​
​
​