Displaying publications 1 - 20 of 62 in total

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  1. 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.
  2. Metabolomics: Challenges and Opportunities in Systems Biology Studies
    Mediani A, Baharum SN
    Methods Mol Biol, 2024;2745:77-90.
    PMID: 38060180 DOI: 10.1007/978-1-0716-3577-3_5
    Metabolomics can provide diagnostic, prognostic, and therapeutic biomarker profiles of individual patients because a large number of metabolites can be simultaneously measured in biological samples in an unbiased manner. Minor stimuli can result in substantial alterations, making it a valuable target for analysis. Due to the complexity and sensitivity of the metabolome, studies must be devised to maintain consistency, minimize subject-to-subject variation, and maximize information recovery. This effort has been aided by technological advances in experimental design, rodent models, and instrumentation. Proton Nuclear Magnetic Resonance (1H-NMR) spectroscopy of biofluids, such as plasma, urine, and faeces provide the opportunity to identify biomarker change patterns that reflect the physiological or pathological status of an individual patient. Metabolomics has the ultimate potential to be useful in a clinical context, where it could be used to predict treatment response and survival and for early disease diagnosis. During drug treatment, an individual's metabolic status could be monitored and used to predict deleterious effects. Therefore, metabolomics has the potential to improve disease diagnosis, treatment, and follow-up care. In this chapter, we demonstrate how a metabolomics study can be used to diagnose a disease by classifying patients as either healthy or pathological, while accounting for individual variation.
  3. Fulltext Seamless and orthogonal expression of genetic parts in polyhydroxyalkanoate (PHA)-producing bacterial chassis for plastic bio-upcycling applications
    Minggu MM, Naseron NAH, Shaberi HSA, Muhammad NAN, Baharum SN, Ramzi AB
    MethodsX, 2023 Dec;11:102434.
    PMID: 37846354 DOI: 10.1016/j.mex.2023.102434
    Polyhydroxyalkanoate (PHA)-producing bacteria represent a powerful synthetic biology chassis for waste bioconversion and bio-upcycling where PHAs can be produced as the final products. In this study, we present a seamless plasmid construction for orthogonal expression of recombinant PET hydrolase (PETase) in model PHA-producing bacteria P. putida and C. necator. To this end, this study described seamless cloning and expression methods utilizing SureVector (SV) system for generating pSV-Ortho-PHA (pSVOP) expression platform in bioengineered P. putida and C. necator. Genetic parts specifically Trc promoter, pBBR1 origin of replication, anchoring proteins and signal sequences were utilized for the transformation of pSVOP-based plasmid in electrocompetent cells and orthogonal expression of PETase in both P. putida and C. necator. Validation steps in confirming functional expression of PETase activity in corresponding PETase-expressing strains were also described to demonstrate seamless and detailed methods in establishing bioengineered P. putida and C. necator as whole-cell biocatalysts tailored for plastic bio-upcycling.•Seamless plasmid construction for orthogonal expression in PHA-producing bacteria.•Step-by-step guide for high-efficiency generation of electrotransformants of P. putida and C. necator.•Adaptable methods for rapid strain development (Design, Build, Test and Learn) for whole-cell biocatalysis.
  4. Fulltext Cloning, Expression and Functional Characterization of a Novel α-Humulene Synthase, Responsible for the Formation of Sesquiterpene in Agarwood Originating from Aquilaria malaccensis
    Sundaraj Y, Abdullah H, Nezhad NG, Rodrigues KF, Sabri S, Baharum SN
    Curr Issues Mol Biol, 2023 Nov 10;45(11):8989-9002.
    PMID: 37998741 DOI: 10.3390/cimb45110564
    This study describes the cloning, expression and functional characterization of α-humulene synthase, responsible for the formation of the key aromatic compound α-humulene in agarwood originating from Aquilaria malaccensis. The partial sesquiterpene synthase gene from the transcriptome data of A. malaccensis was utilized for full-length gene isolation via a 3' RACE PCR. The complete gene, denoted as AmDG2, has an open reading frame (ORF) of 1671 bp and encodes for a polypeptide of 556 amino acids. In silico analysis of the protein highlighted several conserved motifs typically found in terpene synthases such as Asp-rich substrate binding (DDxxD), metal-binding residues (NSE/DTE), and cytoplasmic ER retention (RxR) motifs at their respective sites. The AmDG2 was successfully expressed in the E. coli:pET-28a(+) expression vector whereby an expected band of about 64 kDa in size was detected in the SDS-PAGE gel. In vitro enzyme assay using substrate farnesyl pyrophosphate (FPP) revealed that AmDG2 gave rise to two sesquiterpenes: α-humulene (major) and β-caryophyllene (minor), affirming its identity as α-humulene synthase. On the other hand, protein modeling performed using AlphaFold2 suggested that AmDG2 consists entirely of α-helices with short connecting loops and turns. Meanwhile, molecular docking via AutoDock Vina (Version 1.5.7) predicted that Asp307 and Asp311 act as catalytic residues in the α-humulene synthase. To our knowledge, this is the first comprehensive report on the cloning, expression and functional characterization of α-humulene synthase from agarwood originating from A. malaccensis species. These findings reveal a deeper understanding of the structure and functional properties of the α-humulene synthase and could be utilized for metabolic engineering work in the future.
  5. Fulltext Ethanolic Extract of Polygonum minus Protects Differentiated Human Neuroblastoma Cells (SH-SY5Y) against H2O2-Induced Oxidative Stress
    Sayuti NH, Zulkefli N, Tan JK, Saad N, Baharum SN, Hamezah HS, et al.
    Molecules, 2023 Sep 20;28(18).
    PMID: 37764502 DOI: 10.3390/molecules28186726
    Neuronal models are an important tool in neuroscientific research. Hydrogen peroxide (H2O2), a major risk factor of neuronal oxidative stress, initiates a cascade of neuronal cell death. Polygonum minus Huds, known as 'kesum', is widely used in traditional medicine. P. minus has been reported to exhibit a few medicinal and pharmacological properties. The current study aimed to investigate the neuroprotective effects of P. minus ethanolic extract (PMEE) on H2O2-induced neurotoxicity in SH-SY5Y cells. LC-MS/MS revealed the presence of 28 metabolites in PMEE. Our study showed that the PMEE provided neuroprotection against H2O2-induced oxidative stress by activating the Nrf2/ARE, NF-κB/IκB and MAPK signaling pathways in PMEE pre-treated differentiated SH-SY5Y cells. Meanwhile, the acetylcholine (ACH) level was increased in the oxidative stress-induced treatment group after 4 h of exposure with H2O2. Molecular docking results with acetylcholinesterase (AChE) depicted that quercitrin showed the highest docking score at -9.5 kcal/mol followed by aloe-emodin, afzelin, and citreorosein at -9.4, -9.3 and -9.0 kcal/mol, respectively, compared to the other PMEE's identified compounds, which show lower docking scores. The results indicate that PMEE has neuroprotective effects on SH-SY5Y neuroblastoma cells in vitro. In conclusion, PMEE may aid in reducing oxidative stress as a preventative therapy for neurodegenerative diseases.
  6. Fulltext Oleic acid as potential immunostimulant in metabolism pathways of hybrid grouper fingerlings (Epinephelus fuscoguttatus × Epinephelus lanceolatus) infected with Vibrio vulnificus
    Natnan ME, Low CF, Chong CM, Bunawan H, Baharum SN
    Sci Rep, 2023 Aug 08;13(1):12830.
    PMID: 37553472 DOI: 10.1038/s41598-023-40096-7
    Grouper culture has been expanding in Malaysia due to the huge demand locally and globally. However, due to infectious diseases such as vibriosis, the fish mortality rate increased, which has affected the production of grouper. Therefore, this study focuses on the metabolic profiling of surviving infected grouper fed with different formulations of fatty acid diets that acted as immunostimulants for the fish to achieve desirable growth and health performance. After a six-week feeding trial and one-week post-bacterial challenge, the surviving infected grouper was sampled for GC-MS analysis. For metabolite extraction, a methanol/chloroform/water (2:2:1.8) extraction method was applied to the immune organs (spleen and liver) of surviving infected grouper. The distribution patterns of metabolites between experimental groups were then analyzed using a metabolomics platform. A total of 50 and 81 metabolites were putatively identified from the spleen and liver samples, respectively. Our further analysis identified glycine, serine, and threonine metabolism, and alanine, aspartate and glutamate metabolism had the most impacted pathways, respectively, in spleen and liver samples from surviving infected grouper. The metabolites that were highly abundant in the spleen found in these pathways were glycine (20.9%), l-threonine (1.0%) and l-serine (0.8%). Meanwhile, in the liver l-glutamine (1.8%) and aspartic acid (0.6%) were found to be highly abundant. Interestingly, among the fish diet groups, grouper fed with oleic acid diet produced more metabolites with a higher percent area compared to the control diets. The results obtained from this study elucidate the use of oleic acid as an immunostimulant in fish feed formulation affects more various immune-related metabolites than other formulated feed diets for vibriosis infected grouper.
  7. Molecular cloning and in silico analysis of chalcone isomerase from Polygonum minus
    Shah FLA, Baharum SN, Goh HH, Leow TC, Ramzi AB, Oslan SN, et al.
    Mol Biol Rep, 2023 Jun;50(6):5283-5294.
    PMID: 37148413 DOI: 10.1007/s11033-023-08417-1
    BACKGROUND: Chalcone isomerase (CHI; EC 5.5.1.6) is one of the key enzymes in the flavonoid biosynthetic pathway that is responsible for the intramolecular cyclization of chalcones into specific 2S-flavanones.

    METHODS AND RESULTS: In this study, the open reading frame (ORF) of CHI was successfully isolated from the cDNA of Polygonum minus at 711-bp long, encoding for 236 amino acid residues, with a predicted molecular weight of 25.4 kDa. Multiple sequence alignment and phylogenetic analysis revealed that the conserved residues (Thr50, Tyr108, Asn115, and Ser192) in the cleft of CHI enzyme group active site are present in PmCHI protein sequence and classified as type I. PmCHI comprises more hydrophobic residues without a signal peptide and transmembrane helices. The three-dimensional (3D) structure of PmCHI predicted through homology modeling was validated by Ramachandran plot and Verify3D, with values within the acceptable range of a good model. PmCHI was cloned into pET-28b(+) plasmid, expressed in Escherichia coli BL21(DE3) at 16 °C and partially purified.

    CONCLUSION: These findings contribute to a deeper understanding of the PmCHI protein and its potential for further characterization of its functional properties in the flavonoid biosynthetic pathway.

  8. 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.
  9. Digital Sequence Information and the Access and Benefit-Sharing Obligation of the Convention on Biological Diversity
    Akpoviri FI, Baharum SN, Zainol ZA
    Nanoethics, 2023;17(1):1.
    PMID: 37008389 DOI: 10.1007/s11569-023-00436-3
    With the advent of synthetic biology, scientists are increasingly relying on digital sequence information, instead of physical genetic resources. This article examines the potential impact of this shift on the access and benefit-sharing (ABS) regime of the Convention on Biological Diversity (CBD) and the Nagoya Protocol. These treaties require benefit-sharing with the owners of genetic resources. However, whether "genetic resources" include digital sequence information is unsettled. The CBD conceives genetic resources as genetic material containing functional units of heredity. "Material" implies tangibility, and for some scholars, "functional units of heredity," undefined in both treaties, mean full-coding sequences. This article argues that digital sequence information obtained from physical genetic resources, full-coding or not, should be treated as genetic resources. Literal construction of the CBD risks eroding its usefulness and the ABS regime. This is because through bioinformatics, sequence information can easily be obtained from genetic resources for utilization, without physically moving them or concluding ABS agreement with owners. The CBD must evolve with scientific progress also because sequence functionality depends on the state of knowledge. These arguments are vindicated by domestic ABS laws equating genetic information with genetic resources; Nagoya Protocol provisions deeming research exploiting the genetic composition of genetic resources as utilization of genetic resources; and CBD provisions requiring the sharing of benefits from the utilization of genetic resources. Moreover, treaty interpretation and case law demand that generic, scientific terms, such as "genetic resources" and "functional units of heredity" be interpreted in an evolutionary manner to capture scientific developments.
  10. Fulltext Comparative metabolomics analysis reveals alkaloid repertoires in young and mature Mitragyna speciosa (Korth.) Havil. Leaves
    Veeramohan R, Zamani AI, Azizan KA, Goh HH, Aizat WM, Razak MFA, et al.
    PLoS One, 2023;18(3):e0283147.
    PMID: 36943850 DOI: 10.1371/journal.pone.0283147
    The fresh leaves of Mitragyna speciosa (Korth.) Havil. have been traditionally consumed for centuries in Southeast Asia for its healing properties. Although the alkaloids of M. speciosa have been studied since the 1920s, comparative and systematic studies of metabolite composition based on different leaf maturity levels are still lacking. This study assessed the secondary metabolite composition in two different leaf stages (young and mature) of M. speciosa, using an untargeted liquid chromatography-electrospray ionisation-time-of-flight-mass spectrometry (LC-ESI-TOF-MS) metabolite profiling. The results revealed 86 putatively annotated metabolite features (RT:m/z value) comprising 63 alkaloids, 10 flavonoids, 6 terpenoids, 3 phenylpropanoids, and 1 of each carboxylic acid, glucoside, phenol, and phenolic aldehyde. The alkaloid features were further categorised into 14 subclasses, i.e., the most abundant class of secondary metabolites identified. As per previous reports, indole alkaloids are the most abundant alkaloid subclass in M. speciosa. The result of multivariate analysis (MVA) using principal component analysis (PCA) showed a clear separation of 92.8% between the young and mature leaf samples, indicating a high variance in metabolite levels between them. Akuammidine, alstonine, tryptamine, and yohimbine were tentatively identified among the many new alkaloids reported in this study, depicting the diverse biological activities of M. speciosa. Besides delving into the knowledge of metabolite distribution in different leaf stages, these findings have extended the current alkaloid repository of M. speciosa for a better understanding of its pharmaceutical potential.
  11. Fulltext Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in Vibrio parahaemolyticus
    Yusof NAM, Razali SA, Mohd Padzil A, Lau BYC, Baharum SN, Nor Muhammad NA, et al.
    Biology (Basel), 2022 Nov 01;11(11).
    PMID: 36358301 DOI: 10.3390/biology11111600
    (1) Background: Quorum sensing (QS) is the chemical communication between bacteria that sense chemical signals in the bacterial population to control phenotypic changes through the regulation of gene expression. The inhibition of QS has various potential applications, particularly in the prevention of bacterial infection. QS can be inhibited by targeting the LuxP, a periplasmic receptor protein that is involved in the sensing of the QS signaling molecule known as the autoinducer 2 (AI-2). The sensing of AI-2 by LuxP transduces the chemical information through the inner membrane sensor kinase LuxQ protein and activates the QS cascade. (2) Methods: An in silico approach was applied to design DNA aptamers against LuxP in this study. A method combining molecular docking and molecular dynamics simulations was used to select the oligonucleotides that bind to LuxP, which were then further characterized using isothermal titration calorimetry. Subsequently, the bioactivity of the selected aptamer was examined through comparative transcriptome analysis. (3) Results: Two aptamer candidates were identified from the ITC, which have the lowest dissociation constants (Kd) of 0.2 and 0.5 micromolar. The aptamer with the lowest Kd demonstrated QS suppression and down-regulated the flagellar-assembly-related gene expression. (4) Conclusions: This study developed an in silico approach to design an aptamer that possesses anti-QS properties.
  12. 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.
  13. Fulltext Antibiotic Biosynthesis Pathways from Endophytic Streptomyces SUK 48 through Metabolomics and Genomics Approaches
    Baba MS, Mohamad Zin N, Ahmad SJ, Mazlan NW, Baharum SN, Ahmad N, et al.
    Antibiotics (Basel), 2021 Aug 12;10(8).
    PMID: 34439018 DOI: 10.3390/antibiotics10080969
    Streptomyces sp. has been known to be a major antibiotic producer since the 1940s. As the number of cases related to resistance pathogens infection increases yearly, discovering the biosynthesis pathways of antibiotic has become important. In this study, we present the streamline of a project report summary; the genome data and metabolome data of newly isolated Streptomyces SUK 48 strain are also analyzed. The antibacterial activity of its crude extract is also determined. To obtain genome data, the genomic DNA of SUK 48 was extracted using a commercial kit (Promega) and sent for sequencing (Pac Biosciences technology platform, Menlo Park, CA, USA). The raw data were assembled and polished using Hierarchical Genome Assembly Process 4.0 (HGAP 4.0). The assembled data were structurally predicted using tRNAscan-SE and rnammer. Then, the data were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) database and antiSMASH analysis. Meanwhile, the metabolite profile of SUK 48 was determined using liquid chromatography-mass spectrophotometry (LC-MS) for both negative and positive modes. The results showed that the presence of kanamycin and gentamicin, as well as the other 11 antibiotics. Nevertheless, the biosynthesis pathways of aurantioclavine were also found. The cytotoxicity activity showed IC50 value was at 0.35 ± 1.35 mg/mL on the cell viability of HEK 293. In conclusion, Streptomyces sp. SUK 48 has proven to be a non-toxic antibiotic producer such as auranticlavine and gentamicin.
  14. Fulltext Metabolite profiling of endophytic Streptomyces spp. and its antiplasmodial potential
    Ahmad SJ, Mohamad Zin N, Mazlan NW, Baharum SN, Baba MS, Lau YL
    PeerJ, 2021;9:e10816.
    PMID: 33777509 DOI: 10.7717/peerj.10816
    Background: Antiplasmodial drug discovery is significant especially from natural sources such as plant bacteria. This research aimed to determine antiplasmodial metabolites of Streptomyces spp. against Plasmodium falciparum 3D7 by using a metabolomics approach.

    Methods: Streptomyces strains' growth curves, namely SUK 12 and SUK 48, were measured and P. falciparum 3D7 IC50 values were calculated. Metabolomics analysis was conducted on both strains' mid-exponential and stationary phase extracts.

    Results: The most successful antiplasmodial activity of SUK 12 and SUK 48 extracts shown to be at the stationary phase with IC50 values of 0.8168 ng/mL and 0.1963 ng/mL, respectively. In contrast, the IC50 value of chloroquine diphosphate (CQ) for antiplasmodial activity was 0.2812 ng/mL. The univariate analysis revealed that 854 metabolites and 14, 44 and three metabolites showed significant differences in terms of strain, fermentation phase, and their interactions. Orthogonal partial least square-discriminant analysis and S-loading plot putatively identified pavettine, aurantioclavine, and 4-butyldiphenylmethane as significant outliers from the stationary phase of SUK 48. For potential isolation, metabolomics approach may be used as a preliminary approach to rapidly track and identify the presence of antimalarial metabolites before any isolation and purification can be done.

  15. Fulltext Antimicrobial activities of Bacillus velezensis strains isolated from stingless bee products against methicillin-resistant Staphylococcus aureus
    Baharudin MMA, Ngalimat MS, Mohd Shariff F, Balia Yusof ZN, Karim M, Baharum SN, et al.
    PLoS One, 2021;16(5):e0251514.
    PMID: 33974665 DOI: 10.1371/journal.pone.0251514
    Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have reached epidemic proportions globally. Therefore, there is an urgent need for a continuous supply of antibiotics to combat the problem. In this study, bacteria initially identified as species belonging to the Bacillus amyloliquefaciens operational group were re-identified based on the housekeeping gene, gyrB. Cell-free supernatants (CFS) from the strains were used for antimicrobial tests using the agar well diffusion assay against MRSA and various types of pathogenic bacteria. The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and physicochemical characteristics of the CFS were determined. Based on gyrB sequence analysis, five strains (PD9, B7, PU1, BP1 and L9) were identified as Bacillus velezensis. The CFS of all B. velezensis strains showed broad inhibitory activities against Gram-negative and -positive as well as MRSA strains. Strain PD9 against MRSA ATCC 33742 was chosen for further analysis as it showed the biggest zone of inhibition (21.0 ± 0.4 mm). The MIC and MBC values obtained were 125 μl/ml. The crude antimicrobial extract showed bactericidal activity and was stable at various temperatures (40-80°C), pH (4-12), surfactants (Tween 20, Tween 80, SDS and Triton X-100) and metal ions (MgCI2, NaCI2, ZnNO3 and CuSO4) when tested. However, the crude extract was not stable when treated with proteinase K. All these properties resembled the characteristics of peptides. The antimicrobial compound from the selected strain was purified by using solvent extraction method and silica gel column chromatography. The purified compound was subjected to High Performance Liquid Chromatography which resulted in a single peak of the anti-MRSA compound being detected. The molecular weight of the anti-MRSA compound was determined by using SDS-PAGE and zymogram. The size of the purified antimicrobial peptide was approximately ~ 5 kDa. The antimicrobial peptide produced from B. velezensis strain PD9 is a promising alternative to combat the spread of MRSA infections in the future.
  16. Fulltext Growth modulation and metabolic responses of Ganoderma boninense to salicylic acid stress
    Ong CE, Ahmad R, Goh YK, Azizan KA, Baharum SN, Goh KJ
    PLoS One, 2021;16(12):e0262029.
    PMID: 34972183 DOI: 10.1371/journal.pone.0262029
    Various phenolic compounds have been screened against Ganoderma boninense, the fungal pathogen causing basal stem rot in oil palms. In this study, we focused on the effects of salicylic acid (SA) on the growth of three G. boninense isolates with different levels of aggressiveness. In addition, study on untargeted metabolite profiling was conducted to investigate the metabolomic responses of G. boninense towards salicylic acid. The inhibitory effects of salicylic acid were both concentration- (P < 0.001) and isolate-dependent (P < 0.001). Also, growth-promoting effect was observed in one of the isolates at low concentrations of salicylic acid where it could have been utilized by G. boninense as a source of carbon and energy. Besides, adaptation towards salicylic acid treatment was evident in this study for all isolates, particularly at high concentrations. In other words, inhibitory effect of salicylic acid treatment on the fungal growth declined over time. In terms of metabolomics response to salicylic acid treatment, G. boninense produced several metabolites such as coumarin and azatyrosine, which suggests that salicylic acid modulates the developmental switch in G. boninense towards the defense mode for its survival. Furthermore, the liquid chromatography time-of-flight mass spectrometry (LC-TOF-MS) analysis showed that the growth of G. boninense on potato dextrose agar involved at least four metabolic pathways: amino acid metabolism, lipid pathway, tryptophan pathway and phenylalanine pathway. Overall, there were 17 metabolites that contributed to treatment separation, each with P<0.005. The release of several antimicrobial metabolites such as eudistomin I may enhance G. boninense's competitiveness against other microorganisms during colonisation. Our findings demonstrated the metabolic versatility of G. boninense towards changes in carbon sources and stress factors. G. boninense was shown to be capable of responding to salicylic acid treatment by switching its developmental stage.
  17. Fulltext UPLC-TOF-MS/MS-Based Metabolomics Analysis Reveals Species-Specific Metabolite Compositions in Pitchers of Nepenthes ampullaria, Nepenthes rafflesiana, and Their Hybrid Nepenthes × hookeriana
    Rosli MAF, Mediani A, Azizan KA, Baharum SN, Goh HH
    Front Plant Sci, 2021;12:655004.
    PMID: 33968110 DOI: 10.3389/fpls.2021.655004
    Hybridization is key to the evolution and diversity of plants in nature. Nepenthaceae comprises a family of diverse tropical carnivorous pitcher plant species with extensive hybridization. However, there is no study to date on the metabolite expression of hybrids in this family. We performed a non-targeted metabolomics analysis of the pitchers of two Nepenthes species with different dietary habits, namely, the semi-detritivorous N. ampullaria and carnivorous N. rafflesiana with their hybrid (N. × hookeriana) for a comparative study. The whole-pitcher samples were extracted in methanol:chloroform:water (3:1:1) via sonication-assisted extraction and analyzed using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) followed by data analysis to profile chemical compositions. A total of 1,441 metabolite features were profiled from the three species in which 43.3% of features in the hybrid samples were not found in either of its parents. The partial least squares discriminant analysis (PLS-DA) found 324 metabolite features with variable in projection (VIP) values greater than one in which 55 features were statistically significant. This showed that the hybrid is closer to N. rafflesiana, which is consistent to the previous study on gene and protein expressions. A total of 105 metabolites were putatively identified with manual searches using public metabolite databases. Phenols were detected to be the most abundant secondary metabolites due to a high flavonoid content, especially in N. rafflesiana. The most abundant feature 476.3s:449.102 was found to be the most significant VIP for distinguishing between the three species as a chemical marker. This is the first study comparing metabolites in the carnivory organs of different Nepenthes species with comprehensive profiling and putative identification. The differential metabolite compositions in the pitchers of different species might have ecological implications with the hybrid showing intermediate phenotype between the parents as well as manifesting unique metabolites. However, there is no clear evidence of metabolites related to the differences in dietary habits between the hybrid and the two parent species.
  18. Fulltext Metabolic Profile of Scytalidium parasiticum-Ganoderma boninense Co-Cultures Revealed the Alkaloids, Flavonoids and Fatty Acids that Contribute to Anti-Ganoderma Activity
    Ahmad R, Lim CK, Marzuki NF, Goh YK, Azizan KA, Goh YK, et al.
    Molecules, 2020 Dec 16;25(24).
    PMID: 33339375 DOI: 10.3390/molecules25245965
    In solving the issue of basal stem rot diseases caused by Ganoderma, an investigation of Scytalidium parasiticum as a biological control agent that suppresses Ganoderma infection has gained our interest, as it is more environmentally friendly. Recently, the fungal co-cultivation has emerged as a promising method to discover novel antimicrobial metabolites. In this study, an established technique of co-culturing Scytalidium parasiticum and Ganoderma boninense was applied to produce and induce metabolites that have antifungal activity against G. boninense. The crude extract from the co-culture media was applied to a High Performance Liquid Chromatography (HPLC) preparative column to isolate the bioactive compounds, which were tested against G. boninense. The fractions that showed inhibition against G. boninense were sent for a Liquid Chromatography-Time of Flight-Mass Spectrometry (LC-TOF-MS) analysis to further identify the compounds that were responsible for the microbicidal activity. Interestingly, we found that eudistomin I, naringenin 7-O-beta-D-glucoside and penipanoid A, which were present in different abundances in all the active fractions, except in the control, could be the antimicrobial metabolites. In addition, the abundance of fatty acids, such as oleic acid and stearamide in the active fraction, also enhanced the antimicrobial activity. This comprehensive metabolomics study could be used as the basis for isolating biocontrol compounds to be applied in oil palm fields to combat a Ganoderma infection.
  19. Fulltext The effects of amino acids and fatty acids on the disease resistance of Epinephelus fuscoguttatus in response to Vibrio vulnificus infection
    Nurdalila AA, Natnan ME, Baharum SN
    3 Biotech, 2020 Dec;10(12):544.
    PMID: 33240745 DOI: 10.1007/s13205-020-02543-4
    Mass mortality resulting from bacterial infection poses a major problem in the grouper aquaculture industry. The purpose of this study was to profile the metabolites released in challenged fish and to reconstruct the metabolic pathways of brown marble grouper (Epinephelus fuscoguttatus) in response to Vibrio vulnificus infection. Metabolite profiles from control and challenged treatment groups after feeding were determined using gas chromatography-mass spectrometry (GC-MS). Forty metabolites were identified from the GC-MS analysis. These metabolites comprised of amino acids, fatty acids, organic acids and carbohydrates. The profiles showed the highest percent area (33.1%) for leucine from the amino acid class in infected fish compared to the control treatment group (12.3%). Regarding the fatty acid class, a higher percent area of the metabolite 8,11-eicosadienoic acid (27.04%) was observed in fish infected with V. vulnificus than in the control treatment group (22.5%). Meanwhile, in the carbohydrate class, glucose (47.0%) was the metabolite in the carbohydrate class present at highest percentage in the control treatment group compared to infected fish (30.0%). Our findings highlight the importance of a metabolic analysis for understanding the changes of metabolites in E. fuscoguttatus in response to bacterial infections.
  20. 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.

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