Displaying publications 1 - 20 of 30 in total

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  1. Fulltext Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences
    Bunawan H, Yen CC, Yaakop S, Noor NM
    BMC Res Notes, 2017 Jan 26;10(1):67.
    PMID: 28126013 DOI: 10.1186/s13104-017-2379-1
    The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus.
  2. Fulltext Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey
    Akbar MA, Yusof NYM, Sahrani FK, Usup G, Ahmad A, Baharum SN, et al.
    Biology (Basel), 2021 Aug 25;10(9).
    PMID: 34571703 DOI: 10.3390/biology10090826
    The toxin-producing dinoflagellate Alexandrium minutum is responsible for the outbreaks of harmful algae bloom (HABs). It is a widely distributed species and is responsible for producing paralytic shellfish poisoning toxins. However, the information associated with the environmental adaptation pathway and toxin biosynthesis in this species is still lacking. Therefore, this study focuses on the functional characterization of A. minutum unigenes obtained from transcriptome sequencing using the Illumina Hiseq 4000 sequencing platform. A total of 58,802 (47.05%) unigenes were successfully annotated using public databases such as NCBI-Nr, UniprotKB, EggNOG, KEGG, InterPRO and Gene Ontology (GO). This study has successfully identified key features that enable A. minutum to adapt to the marine environment, including several carbon metabolic pathways, assimilation of various sources of nitrogen and phosphorus. A. minutum was found to encode homologues for several proteins involved in saxitoxin biosynthesis, including the first three proteins in the pathway of saxitoxin biosynthesis, namely sxtA, sxtG and sxtB. The comprehensive transcriptome analysis presented in this study represents a valuable resource for understanding the dinoflagellates molecular metabolic model regarding nutrient acquisition and biosynthesis of saxitoxin.
  3. Fulltext An insight review on the neuropharmacological effects, mechanisms of action, pharmacokinetics and toxicity of mitragynine
    Annuar NAK, Azlan UK, Mediani A, Tong X, Han R, Al-Olayan E, et al.
    Biomed Pharmacother, 2024 Feb;171:116134.
    PMID: 38219389 DOI: 10.1016/j.biopha.2024.116134
    Mitragynine is one of the main psychoactive alkaloids in Mitragyna speciosa Korth. (kratom). It has opium-like effects by acting on μ-, δ-, and κ-opioid receptors in the brain. The compound also interacts with other receptors, such as adrenergic and serotonergic receptors and neuronal Ca2+ channels in the central nervous system to have its neuropharmacological effects. Mitragynine has the potential to treat diseases related to neurodegeneration such as Alzheimer's disease and Parkinson's disease, as its modulation on the opioid receptors has been reported extensively. This review aimed to provide an up-to-date and critical overview on the neuropharmacological effects, mechanisms of action, pharmacokinetics and safety of mitragynine as a prospective psychotropic agent. Its multiple neuropharmacological effects on the brain include antinociceptive, anti-inflammatory, antidepressant, sedative, stimulant, cognitive, and anxiolytic activities. The potential of mitragynine to manage opioid withdrawal symptoms related to opioid dependence, its pharmacokinetics and toxic effects were also discussed. The interaction of mitragynine with various receptors in the brain produce diverse neuropharmacological effects, which have beneficial properties in neurological disorders. However, further studies need to be carried out on mitragynine to uncover its complex mechanisms of action, pharmacokinetics, pharmacodynamic profiles, addictive potential, and safe dosage to prevent harmful side effects.
  4. Fulltext Dataset of Fourier transform-infrared coupled with chemometric analysis used to distinguish accessions of Garcinia mangostana L. in Peninsular Malaysia
    Samsir SA, Bunawan H, Yen CC, Noor NM
    Data Brief, 2016 Sep;8:1-5.
    PMID: 27257614 DOI: 10.1016/j.dib.2016.04.062
    In this dataset, we distinguish 15 accessions of Garcinia mangostana from Peninsular Malaysia using Fourier transform-infrared spectroscopy coupled with chemometric analysis. We found that the position and intensity of characteristic peaks at 3600-3100 cm(-) (1) in IR spectra allowed discrimination of G. mangostana from different locations. Further principal component analysis (PCA) of all the accessions suggests the two main clusters were formed: samples from Johor, Melaka, and Negeri Sembilan (South) were clustered together in one group while samples from Perak, Kedah, Penang, Selangor, Kelantan, and Terengganu (North and East Coast) were in another clustered group.
  5. Fulltext Data set of phylogenetic analysis inferred based on the complete genomes of the family Nodaviridae
    Low CF, Bunawan H
    Data Brief, 2016 Sep;8:1454-61.
    PMID: 27617282 DOI: 10.1016/j.dib.2016.08.025
    In this article, nine complete genomes of viruses from the genus Alphanodavirus and Betanodavirus (Family Nodaviridae) were comparatively analyzed and the data of their evolutionary origins and relatedness are reported. The nucleotide sequence alignment of the complete genomes from all species and their deduced evolutionary relationships are presented. High sequence similarity within the genus Betanodavirus compared to the genus Alphanodavirus was revealed in multiple sequence alignment of the Nodaviridae genomes. The amino acid sequence similarity for both RNA1 and RNA2 ORF is more conserved in Betanodavirus, compared to Alphanodavirus. The conserved and variable regions within the virus genome that were defined based on the multiple sequence alignments are presented in this dataset.
  6. Fulltext Dataset of SSR markers for ISSR-Suppression-PCR to detect genetic variation in Garcinia mangostana L. in Peninsular Malaysia
    Samsir SA, Bunawan H, Yen CC, Noor NM
    Data Brief, 2016 Sep;8:1438-42.
    PMID: 27617279 DOI: 10.1016/j.dib.2016.08.016
    In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia.
  7. Fulltext Data on Fourier transform-infrared of Cosmos caudatus Kunth. tissues analyzed with chemometric analysis
    Gunasekaran D, Bunawan H, Ismail I, Noor NM
    Data Brief, 2018 Aug;19:1423-1427.
    PMID: 30229014 DOI: 10.1016/j.dib.2018.06.025
    In this dataset, we differentiate four different tissues of Cosmos caudatus Kunth (leaves, flowers, stem and root) obtained from UKM Bangi plot, based on Fourier transform-infrared spectroscopy. Different tissues of C. caudatus demonstrated the position and intensity of characteristic peaks at 4000-450 cm-1. Principal component analysis (PCA) shows three main groups were formed. The samples from leaves and flowers were found to be clustered together in one group, while the samples from stems and roots were clustered into two separate groups, respectively. This data provides an insight into the fingerprint identification and distribution of metabolites in the different organs of this species.
  8. Fulltext Sauropus androgynus (L.) Merr. Induced Bronchiolitis Obliterans: From Botanical Studies to Toxicology
    Bunawan H, Bunawan SN, Baharum SN, Noor NM
    Evid Based Complement Alternat Med, 2015;2015:714158.
    PMID: 26413127 DOI: 10.1155/2015/714158
    Sauropus androgynus L. Merr. is one of the most popular herbs in South Asia, Southeast Asia, and China where it was known as a slimming agent until two outbreaks of pulmonary dysfunction were reported in Taiwan and Japan in 1995 and 2005, respectively. Several studies described that the excessive consumption of Sauropus androgynus could cause drowsiness, constipation, and bronchiolitis obliterans and may lead to respiratory failure. Interestingly, this herb has been used in Malaysia and Indonesia in cooking and is commonly called the "multigreen" or "multivitamin" plant due to its high nutritive value and inexpensive source of dietary protein. The plant is widely used in traditional medicine for wound healing, inducing lactation, relief of urinary disorders, as an antidiabetic cure and also fever reduction. Besides these medicinal uses, the plant can also be used as colouring agent in food. This review will explore and compile the fragmented knowledge available on the botany, ethnobotany, chemical constitutes, pharmacological properties, and toxicological aspects of this plant. This comprehensive review will give readers the fundamental, comprehensive, and current knowledge regarding Sauropus androgynus L. Merr.
  9. Fulltext Ficus deltoidea Jack: A Review on Its Phytochemical and Pharmacological Importance
    Bunawan H, Amin NM, Bunawan SN, Baharum SN, Mohd Noor N
    Evid Based Complement Alternat Med, 2014;2014:902734.
    PMID: 24772185 DOI: 10.1155/2014/902734
    Ficus deltoidea Jack (Moraceae) has had a long history of use in traditional medicine among the Malays to alleviate and heal ailments such as sores, wounds, and rheumatism and as an after-birth tonic and an antidiabetic drug. Modern pharmacological studies demonstrated that this plant has a wide variety of beneficial attributes for human health. Despite its importance, a review of this species has not been published in the scientific literature to date. Here, we review and summarize the historic and current literature concerning the botany, traditional uses, phytochemistry, pharmacological effects, and toxicity of this wonder plant. This summary could be beneficial for future research aiming to exploit the therapeutic potential of this useful, medicinal species.
  10. Fulltext Streamlining Natural Products Biomanufacturing With Omics and Machine Learning Driven Microbial Engineering
    Ramzi AB, Baharum SN, Bunawan H, Scrutton NS
    Front Bioeng Biotechnol, 2020;8:608918.
    PMID: 33409270 DOI: 10.3389/fbioe.2020.608918
    Increasing demands for the supply of biopharmaceuticals have propelled the advancement of metabolic engineering and synthetic biology strategies for biomanufacturing of bioactive natural products. Using metabolically engineered microbes as the bioproduction hosts, a variety of natural products including terpenes, flavonoids, alkaloids, and cannabinoids have been synthesized through the construction and expression of known and newly found biosynthetic genes primarily from model and non-model plants. The employment of omics technology and machine learning (ML) platforms as high throughput analytical tools has been increasingly leveraged in promoting data-guided optimization of targeted biosynthetic pathways and enhancement of the microbial production capacity, thereby representing a critical debottlenecking approach in improving and streamlining natural products biomanufacturing. To this end, this mini review summarizes recent efforts that utilize omics platforms and ML tools in strain optimization and prototyping and discusses the beneficial uses of omics-enabled discovery of plant biosynthetic genes in the production of complex plant-based natural products by bioengineered microbes.
  11. Fulltext A comprehensive review of drying meat products and the associated effects and changes
    Mediani A, Hamezah HS, Jam FA, Mahadi NF, Chan SXY, Rohani ER, et al.
    Front Nutr, 2022;9:1057366.
    PMID: 36518998 DOI: 10.3389/fnut.2022.1057366
    Preserving fresh food, such as meat, is significant in the effort of combating global food scarcity. Meat drying is a common way of preserving meat with a rich history in many cultures around the globe. In modern days, dried meat has become a well enjoyed food product in the market because of its long shelf-life, taste and health benefits. This review aims to compile information on how the types of meat, ingredients and the used drying technologies influence the characteristics of dried meat in physicochemical, microbial, biochemical and safety features along with technological future prospects in the dried meat industry. The quality of dried meat can be influenced by a variety of factors, including its production conditions and the major biochemical changes that occur throughout the drying process, which are also discussed in this review. Additionally, the sensory attributes of dried meat are also reviewed, whereby the texture of meat and the preference of the market are emphasized. There are other aspects and concerning issues that are suggested for future studies. It is well-known that reducing the water content in meat helps in preventing microbial growth, which in turn prevents the presence of harmful substances in meat. However, drying the meat can change the characteristics of the meat itself, making consumers concerned on whether dried meat is safe to be consumed on a regular basis. It is important to consider the role of microbial enzymes and microbes in the preservation of their flavor when discussing dried meats and dried meat products. The sensory, microbiological, and safety elements of dried meat are also affected by these distinctive changes, which revolve around customer preferences and health concerns, particularly how drying is efficient in eliminating/reducing hazardous bacteria from the fish. Interestingly, some studies have concentrated on increasing the efficiency of dried meat production to produce a safer range of dried meat products with less effort and time. This review compiled important information from all available online research databases. This review may help the food sector in improving the efficiency and safety of meat drying, reducing food waste, while maintaining the quality and nutritional content of dried meat.
  12. Fulltext Molecular systematics of Polygonum minus Huds. based on ITS sequences
    Bunawan H, Choong CY, Md-Zain BM, Baharum SN, Noor NM
    Int J Mol Sci, 2011;12(11):7626-34.
    PMID: 22174621 DOI: 10.3390/ijms12117626
    Plastid trnL-trnF and nuclear ribosomal ITS sequences were obtained from selected wild-type individuals of Polygonum minus Huds. in Peninsular Malaysia. The 380 bp trnL-trnF sequences of the Polygonum minus accessions were identical. Therefore, the trnL-trnF failed to distinguish between the Polygonum minus accessions. However, the divergence of ITS sequences (650 bp) among the Polygonum minus accessions was 1%, indicating that these accessions could be distinguished by the ITS sequences. A phylogenetic relationship based on the ITS sequences was inferred using neighbor-joining, maximum parsimony and Bayesian inference. All of the tree topologies indicated that Polygonum minus from Peninsular Malaysia is unique and different from the synonymous Persicaria minor (Huds.) Opiz and Polygonum kawagoeanum Makino.
  13. Fulltext Erwinia mallotivora sp., a new pathogen of papaya (Carica papaya) in Peninsular Malaysia
    Amin NM, Bunawan H, Redzuan RA, Jaganath IB
    Int J Mol Sci, 2010;12(1):39-45.
    PMID: 21339975 DOI: 10.3390/ijms12010039
    Erwinia mallotivora was isolated from papaya infected with dieback disease showing the typical symptoms of greasy, water-soaked lesions and spots on leaves. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the genus Erwinia and was united in a monophyletic group with E. mallotivora DSM 4565 (AJ233414). Earlier studies had indicated that the causal agent for this disease was E. papayae. However, our current studies, through Koch's postulate, have confirmed that papaya dieback disease is caused by E. mallotivora. To our knowledge, this is the first new discovery of E. mallotivora as a causal agent of papaya dieback disease in Peninsular Malaysia. Previous reports have suggested that E. mallotivora causes leaf spot in Mallotus japonicus. However, this research confirms it also to be pathogenic to Carica papaya.
  14. Fulltext Flavonoids as Potential Wound-Healing Molecules: Emphasis on Pathways Perspective
    Zulkefli N, Che Zahari CNM, Sayuti NH, Kamarudin AA, Saad N, Hamezah HS, et al.
    Int J Mol Sci, 2023 Feb 27;24(5).
    PMID: 36902038 DOI: 10.3390/ijms24054607
    Wounds are considered to be a serious problem that affects the healthcare sector in many countries, primarily due to diabetes and obesity. Wounds become worse because of unhealthy lifestyles and habits. Wound healing is a complicated physiological process that is essential for restoring the epithelial barrier after an injury. Numerous studies have reported that flavonoids possess wound-healing properties due to their well-acclaimed anti-inflammatory, angiogenesis, re-epithelialization, and antioxidant effects. They have been shown to be able to act on the wound-healing process via expression of biomarkers respective to the pathways that mainly include Wnt/β-catenin, Hippo, Transforming Growth Factor-beta (TGF-β), Hedgehog, c-Jun N-Terminal Kinase (JNK), NF-E2-related factor 2/antioxidant responsive element (Nrf2/ARE), Nuclear Factor Kappa B (NF-κB), MAPK/ERK, Ras/Raf/MEK/ERK, phosphatidylinositol 3-kinase (PI3K)/Akt, Nitric oxide (NO) pathways, etc. Hence, we have compiled existing evidence on the manipulation of flavonoids towards achieving skin wound healing, together with current limitations and future perspectives in support of these polyphenolic compounds as safe wound-healing agents, in this review.
  15. Fulltext Homogeneous Nature of Malaysian Marine Fish Epinephelus fuscoguttatus (Perciformes; Serranidae): Evidence Based on Molecular Markers, Morphology and Fourier Transform Infrared Analysis
    Nurdalila AA, Bunawan H, Kumar SV, Rodrigues KF, Baharum SN
    Int J Mol Sci, 2015 Jul 02;16(7):14884-900.
    PMID: 26147421 DOI: 10.3390/ijms160714884
    Taxonomic confusion exists within the genus Epinephelus due to the lack of morphological specializations and the overwhelming number of species reported in several studies. The homogenous nature of the morphology has created confusion in the Malaysian Marine fish species Epinephelus fuscoguttatus and Epinephelus hexagonatus. In this study, the partial DNA sequence of the 16S gene and mitochondrial nucleotide sequences of two gene regions, Cytochrome Oxidase Subunit I and III were used to investigate the phylogenetic relationship between them. In the phylogenetic trees, E. fuscoguttatus was monophyletic with E. hexagonatus species and morphology examination shows that no significant differences were found in the morphometric features between these two taxa. This suggests that E. fuscoguttatus is not distinguishable from E. hexagonatus species, and that E. fuscoguttatus have been identified to be E. hexagonatus species is likely attributed to differences in environment and ability to camouflage themselves under certain conditions. Interestingly, this finding was also supported by Principal Component Analysis on Attenuated Total Reflectance-Fourier-transform Infrared (ATR-FTIR) data analysis. Molecular, morphological and meristic characteristics were combined with ATR-FTIR analysis used in this study offer new perspectives in fish species identification. To our knowledge, this is the first report of an extensive genetic population study of E. fuscoguttatus in Malaysia and this understanding will play an important role in informing genetic stock-specific strategies for the management and conservation of this highly valued fish.
  16. Fulltext Papaya Dieback in Malaysia: A Step Towards A New Insight of Disease Resistance
    Bunawan H, Baharum SN
    Iran J Biotechnol, 2015 Dec;13(4):1-2.
    PMID: 28959302 DOI: 10.15171/ijb.1139
  17. Fulltext Sequence and Phylogenetic Analysis of the First Complete Genome of Ricetungro spherical virus in Malaysia
    Kannan M, Mohamad Saad M, Zainal Z, Kassim H, Ismail I, Talip N, et al.
    Iran J Biotechnol, 2020 Oct;18(4):e2566.
    PMID: 34056024 DOI: 10.30498/IJB.2020.2566
    Background: Rice tungro disease (RTD) is a viral disease mainly affecting rice in Asia. RTD caused by Rice tungro bacilliform virus and Rice tungro spherical virus. To date, there are only 5 RTSV isolates have been reported.

    Objectives: In this study, we aimed to report the complete nucleotide sequence of Malaysian isolate of Rice tungro spherical virus Seberang Perai (RTSV-SP) for the first time. RTSV-SP was characterized and its evolutionary relationship with previously reported Indian and Philippines isolates were elucidated.

    Materials and Methods: RTSV-SP isolate was isolated from a recent outbreak in a paddy field in Seberang Perai zone of Malaysia. Its complete genome was amplified by RT-PCR, cloned and sequenced.

    Results: Sequence analysis indicated that the genome of RTSV-SP consisted of 12,173 nucleotides (nt). Comparative analysis of 6 complete genome sequences using Clustal Omega showed that Seberang Perai isolate shared the highest nucleotide identity (96.04%) with Philippine-A isolate, except that the sORF-2 of RTSV-SP is shorter than RTSV Philippine-A by 27 amino acid residues. RTSV-SP found to cluster in Southeast Asia (SEA) group based on the whole genome sequence phylogenetic analysis using MEGA X software.

    Conclusions: Phylogenetic classification of RTSV isolates based on the complete nucleotide sequences showed more distinctive clustering pattern with the addition of RTSV-SP whole genome to the available isolates. Present study described the isolation and molecular characterization of RTSV-SP.

  18. Current advancements in systems and synthetic biology studies of Saccharomyces cerevisiae
    Ting TY, Li Y, Bunawan H, Ramzi AB, Goh HH
    J Biosci Bioeng, 2023 Apr;135(4):259-265.
    PMID: 36803862 DOI: 10.1016/j.jbiosc.2023.01.010
    Saccharomyces cerevisiae has a long-standing history of biotechnological applications even before the dawn of modern biotechnology. The field is undergoing accelerated advancement with the recent systems and synthetic biology approaches. In this review, we highlight the recent findings in the field with a focus on omics studies of S. cerevisiae to investigate its stress tolerance in different industries. The latest advancements in S. cerevisiae systems and synthetic biology approaches for the development of genome-scale metabolic models (GEMs) and molecular tools such as multiplex Cas9, Cas12a, Cpf1, and Csy4 genome editing tools, modular expression cassette with optimal transcription factors, promoters, and terminator libraries as well as metabolic engineering. Omics data analysis is key to the identification of exploitable native genes/proteins/pathways in S. cerevisiae with the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.
  19. Fulltext Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective
    Akbar MA, Mohd Yusof NY, Tahir NI, Ahmad A, Usup G, Sahrani FK, et al.
    Mar Drugs, 2020 Feb 05;18(2).
    PMID: 32033403 DOI: 10.3390/md18020103
    Saxitoxin is an alkaloid neurotoxin originally isolated from the clam Saxidomus giganteus in 1957. This group of neurotoxins is produced by several species of freshwater cyanobacteria and marine dinoflagellates. The saxitoxin biosynthesis pathway was described for the first time in the 1980s and, since then, it was studied in more than seven cyanobacterial genera, comprising 26 genes that form a cluster ranging from 25.7 kb to 35 kb in sequence length. Due to the complexity of the genomic landscape, saxitoxin biosynthesis in dinoflagellates remains unknown. In order to reveal and understand the dynamics of the activity in such impressive unicellular organisms with a complex genome, a strategy that can carefully engage them in a systems view is necessary. Advances in omics technology (the collective tools of biological sciences) facilitated high-throughput studies of the genome, transcriptome, proteome, and metabolome of dinoflagellates. The omics approach was utilized to address saxitoxin-producing dinoflagellates in response to environmental stresses to improve understanding of dinoflagellates gene-environment interactions. Therefore, in this review, the progress in understanding dinoflagellate saxitoxin biosynthesis using an omics approach is emphasized. Further potential applications of metabolomics and genomics to unravel novel insights into saxitoxin biosynthesis in dinoflagellates are also reviewed.
  20. Pathogenic hitchhiker diversity on international ships' ballast water at West Malaysia port
    Salleh NA, Rosli FN, Akbar MA, Yusof A, Sahrani FK, Razak SA, et al.
    Mar Pollut Bull, 2021 Nov;172:112850.
    PMID: 34391012 DOI: 10.1016/j.marpolbul.2021.112850
    This study investigates bacterial diversity and potential pathogens in the international ships' ballast water at Tanjung Pelepas Port, Malaysia, using 16S rRNA amplicon sequencing. Thirty-four bacterial phylum, 305 families, 577 genera, and 941 species were detected in eight ballast water samples of different origins. The similarity of the bacterial composition between samples was found to be random and not tied to geographical locations. The bacterial abundance did not seem to be affected by related physicochemical except for temperature. Ballast water samples with a temperature lower than 25 °C showed a relatively lower bacterial abundance. A total of 33 potential pathogens were detected from all ballast water samples. Pseudomonas spp., Tenacibaculum spp., Flavobacteriaceae spp., Halomonas spp., and Acinetobacter junii are the potential pathogens with more than 10% OTU prevalence. This study would provide beneficial information for further enhancing ballast water microorganism guidelines in Malaysia.
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