Displaying publications 1 - 20 of 30 in total

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  1. Characterization of promoter of EgPAL1, a novel PAL gene from the oil palm Elaeis guineensis Jacq
    Yusuf CYL, Abdullah JO, Shaharuddin NA, Abu Seman I, Abdullah MP
    Plant Cell Rep, 2018 Feb;37(2):265-278.
    PMID: 29090330 DOI: 10.1007/s00299-017-2228-7
    KEY MESSAGE: The oil palm EgPAL1 gene promoter and its regulatory region were functional as a promoter in the heterologous system of Arabidopsis according to the cis-acting elements present in that region. The promoter was developmentally regulated, vascular tissue specific and responsive to water stress agents. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the key enzyme of the phenylpropanoid pathway which plays important roles in plant development and adaptation. To date, there is no report on the study of PAL from oil palm (Elaeis guineensis), an economically important oil crop. In this study, the 5' regulatory sequence of a highly divergent oil palm PAL gene (EgPAL1) was isolated and fused with GUS in Arabidopsis to create two transgenic plants carrying the minimal promoter with (2302 bp) and without its regulatory elements (139 bp). The regulatory sequence contained cis-acting elements known to be important for plant development and stress response including the AC-II element for lignin biosynthesis and several stress responsive elements. The promoter and its regulatory region were fully functional in Arabidopsis. Its activities were characterised by two common fundamental features of PAL which are responsive to plant internal developmental programme and external factors. The promoter was developmentally regulated in certain organs; highly active in young organs but less active or inactive in mature organs. The presence of the AC elements and global activity of the EgPAL1 promoter in all organs resembled the property of lignin-related genes. The existence of the MBS element and enhancement of the promoter activity by PEG reflected the behaviour of drought-responsive genes. Our findings provide a platform for evaluating oil palm gene promoters in the heterologous system of Arabidopsis and give insights into the activities of EgPAL1 promoter in oil palm.
  2. Fulltext Induction, Multiplication, and Evaluation of Antioxidant Activity of Polyalthia bullata Callus, a Woody Medicinal Plant
    Kamarul Zaman MA, Azzeme AM, Ramle IK, Normanshah N, Ramli SN, Shaharuddin NA, et al.
    Plants (Basel), 2020 Dec 14;9(12).
    PMID: 33327608 DOI: 10.3390/plants9121772
    Polyalthia bullata is an endangered medicinal plant species. Hence, establishment of P. bullata callus culture is hoped to assist in mass production of secondary metabolites. Leaf and midrib were explants for callus induction. Both of them were cultured on Murashige and Skoog (MS) and Woody Plant Medium (WPM) containing different types and concentrations of auxins (2,4-dichlorophenoxyacetic acid (2,4-D), α-naphthaleneacetic acid (NAA), picloram, and dicamba). The callus produced was further multiplied on MS and WPM supplemented with different concentrations of 2,4-D, NAA, picloram, dicamba, indole-3-acetic acid (IAA), and indole-3-butyric acid (IBA) media. The quantification of total phenolic content (TPC), total flavonoid content (TFC) and antioxidant capacity was further carried out on P. bullata callus, and the results were subjected to correlation analysis. Among the media, the WPM + 16.56 µM picloram (53.33 ± 22.06%) was the best for callus induction while MS + 30 µM dicamba was the best for callus multiplication. The TPC, TFC, and EC50 of DPPH scavenging activity were determined at 0.657 ± 0.07 mg GAE/g FW, 0.491 ± 0.03 mg QE/g, and 85.59 ± 6.09 µg/mL in P. bullata callus, respectively. The positive correlation between DPPH scavenging activity with TPC was determined at r = 0.869, and that of TFC was at r = 0.904. Hence, the P. bullata callus has an ability to accumulate antioxidants. It therefore can be a medium for secondary metabolites production.
  3. Fulltext Hexavalent molybdenum reduction to mo-blue by a sodium-dodecyl-sulfate-degrading Klebsiella oxytoca strain DRY14
    Halmi MI, Zuhainis SW, Yusof MT, Shaharuddin NA, Helmi W, Shukor Y, et al.
    Biomed Res Int, 2013;2013:384541.
    PMID: 24383052 DOI: 10.1155/2013/384541
    Bacteria with the ability to tolerate, remove, and/or degrade several xenobiotics simultaneously are urgently needed for remediation of polluted sites. A previously isolated bacterium with sodium dodecyl sulfate- (SDS-) degrading capacity was found to be able to reduce molybdenum to the nontoxic molybdenum blue. The optimal pH, carbon source, molybdate concentration, and temperature supporting molybdate reduction were pH 7.0, glucose at 1.5% (w/v), between 25 and 30 mM, and 25°C, respectively. The optimum phosphate concentration for molybdate reduction was 5 mM. The Mo-blue produced exhibits an absorption spectrum with a maximum peak at 865 nm and a shoulder at 700 nm. None of the respiratory inhibitors tested showed any inhibition to the molybdenum-reducing activity suggesting that the electron transport system of this bacterium is not the site of molybdenum reduction. Chromium, cadmium, silver, copper, mercury, and lead caused approximately 77, 65, 77, 89, 80, and 80% inhibition of the molybdenum-reducing activity, respectively. Ferrous and stannous ions markedly increased the activity of molybdenum-reducing activity in this bacterium. The maximum tolerable concentration of SDS as a cocontaminant was 3 g/L. The characteristics of this bacterium make it a suitable candidate for molybdenum bioremediation of sites cocontaminated with detergent pollutant.
  4. Fulltext Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07
    Lee GLY, Zakaria NN, Convey P, Futamata H, Zulkharnain A, Suzuki K, et al.
    Int J Mol Sci, 2020 Dec 09;21(24).
    PMID: 33316871 DOI: 10.3390/ijms21249363
    Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica.
  5. Fulltext A Review and Bibliometric Analysis on Applications of Microbial Degradation of Hydrocarbon Contaminants in Arctic Marine Environment at Metagenomic and Enzymatic Levels
    Verasoundarapandian G, Wong CY, Shaharuddin NA, Gomez-Fuentes C, Zulkharnain A, Ahmad SA
    Int J Environ Res Public Health, 2021 02 09;18(4).
    PMID: 33572432 DOI: 10.3390/ijerph18041671
    The globe is presently reliant on natural resources, fossil fuels, and crude oil to support the world's energy requirements. Human exploration for oil resources is always associated with irreversible effects. Primary sources of hydrocarbon pollution are instigated through oil exploration, extraction, and transportation in the Arctic region. To address the state of pollution, it is necessary to understand the mechanisms and processes of the bioremediation of hydrocarbons. The application of various microbial communities originated from the Arctic can provide a better interpretation on the mechanisms of specific microbes in the biodegradation process. The composition of oil and consequences of hydrocarbon pollutants to the various marine environments are also discussed in this paper. An overview of emerging trends on literature or research publications published in the last decade was compiled via bibliometric analysis in relation to the topic of interest, which is the microbial community present in the Arctic and Antarctic marine environments. This review also presents the hydrocarbon-degrading microbial community present in the Arctic, biodegradation metabolic pathways (enzymatic level), and capacity of microbial degradation from the perspective of metagenomics. The limitations are stated and recommendations are proposed for future research prospects on biodegradation of oil contaminants by microbial community at the low temperature regions of the Arctic.
  6. Fulltext Diesel in Antarctica and a Bibliometric Study on Its Indigenous Microorganisms as Remediation Agent
    Wong RR, Lim ZS, Shaharuddin NA, Zulkharnain A, Gomez-Fuentes C, Ahmad SA
    Int J Environ Res Public Health, 2021 02 05;18(4).
    PMID: 33562609 DOI: 10.3390/ijerph18041512
    Diesel acts as a main energy source to complement human activities in Antarctica. However, the increased expedition in Antarctica has threatened the environment as well as its living organisms. While more efforts on the use of renewable energy are being done, most activities in Antarctica still depend heavily on the use of diesel. Diesel contaminants in their natural state are known to be persistent, complex and toxic. The low temperature in Antarctica worsens these issues, making pollutants more significantly toxic to their environment and indigenous organisms. A bibliometric analysis had demonstrated a gradual increase in the number of studies on the microbial hydrocarbon remediation in Antarctica over the year. It was also found that these studies were dominated by those that used bacteria as remediating agents, whereas very little focus was given on fungi and microalgae. This review presents a summary of the collective and past understanding to the current findings of Antarctic microbial enzymatic degradation of hydrocarbons as well as its genotypic adaptation to the extreme low temperature.
  7. Fulltext Toward a Better Understanding of Metal Nanoparticles, a Novel Strategy from Eucalyptus Plants
    Sawalha H, Abiri R, Sanusi R, Shaharuddin NA, Noor AAM, Ab Shukor NA, et al.
    Plants (Basel), 2021 May 07;10(5).
    PMID: 34066925 DOI: 10.3390/plants10050929
    Nanotechnology is a promising tool that has opened the doors of improvement to the quality of human's lives through its potential in numerous technological aspects. Green chemistry of nanoscale materials (1-100 nm) is as an effective and sustainable strategy to manufacture homogeneous nanoparticles (NPs) with unique properties, thus making the synthesis of green NPs, especially metal nanoparticles (MNPs), the scientist's core theme. Researchers have tested different organisms to manufacture MNPs and the results of experiments confirmed that plants tend to be the ideal candidate amongst all entities and are suitable to synthesize a wide variety of MNPs. Natural and cultivated Eucalyptus forests are among woody plants used for landscape beautification and as forest products. The present review has been written to reflect the efficacious role of Eucalyptus in the synthesis of MNPs. To better understand this, the route of extracting MNPs from plants, in general, and Eucalyptus, in particular, are discussed. Furthermore, the crucial factors influencing the process of MNP synthesis from Eucalyptus as well as their characterization and recent applications are highlighted. Information gathered in this review is useful to build a basis for new prospective research ideas on how to exploit this woody species in the production of MNPs. Nevertheless, there is a necessity to feed the scientific field with further investigations on wider applications of Eucalyptus-derived MNPs.
  8. Fulltext Statistical Optimisation of Diesel Biodegradation at Low Temperatures by an Antarctic Marine Bacterial Consortium Isolated from Non-Contaminated Seawater
    Zakaria NN, Gomez-Fuentes C, Abdul Khalil K, Convey P, Roslee AFA, Zulkharnain A, et al.
    Microorganisms, 2021 Jun 03;9(6).
    PMID: 34205164 DOI: 10.3390/microorganisms9061213
    Hydrocarbon pollution is widespread around the globe and, even in the remoteness of Antarctica, the impacts of hydrocarbons from anthropogenic sources are still apparent. Antarctica's chronically cold temperatures and other extreme environmental conditions reduce the rates of biological processes, including the biodegradation of pollutants. However, the native Antarctic microbial diversity provides a reservoir of cold-adapted microorganisms, some of which have the potential for biodegradation. This study evaluated the diesel hydrocarbon-degrading ability of a psychrotolerant marine bacterial consortium obtained from the coast of the north-west Antarctic Peninsula. The consortium's growth conditions were optimised using one-factor-at-a-time (OFAT) and statistical response surface methodology (RSM), which identified optimal growth conditions of pH 8.0, 10 °C, 25 ppt NaCl and 1.5 g/L NH4NO3. The predicted model was highly significant and confirmed that the parameters' salinity, temperature, nitrogen concentration and initial diesel concentration significantly influenced diesel biodegradation. Using the optimised values generated by RSM, a mass reduction of 12.23 mg/mL from the initial 30.518 mg/mL (4% (w/v)) concentration of diesel was achieved within a 6 d incubation period. This study provides further evidence for the presence of native hydrocarbon-degrading bacteria in non-contaminated Antarctic seawater.
  9. Fulltext Effects of Diesel, Heavy Metals and Plastics Pollution on Penguins in Antarctica: A Review
    Puasa NA, Zulkharnain A, Verasoundarapandian G, Wong CY, Zahri KNM, Merican F, et al.
    Animals (Basel), 2021 Aug 26;11(9).
    PMID: 34573474 DOI: 10.3390/ani11092505
    Antarctica is a relatively pristine continent that attracts scientists and tourists alike. However, the risk of environmental pollution in Antarctica is increasing with the increase in the number of visitors. Recently, there has been a surge in interest regarding diesel, heavy metals and microplastics pollution. Contamination from these pollutants poses risks to the environment and the health of organisms inhabiting the continent. Penguins are one of the most prominent and widely distributed animals in Antarctica and are at major risk due to pollution. Even on a small scale, the impacts of pollution toward penguin populations are extensive. This review discusses the background of penguins in Antarctica, the anthropogenic pollution and cases, as well as the impacts of diesel, heavy metals and microplastics toxicities on penguins. The trends of the literature for the emerging risks of these pollutants are also reviewed through a bibliometric approach and network mapping analysis. A sum of 27 articles are analyzed on the effects of varying pollutants on penguins in Antarctica from 2000 to 2020 using the VOSviewer bibliometric software, Microsoft Excel and Tableau Public. Research articles collected from the Scopus database are evaluated for the most applicable research themes according to the bibliometric indicators (articles, geography distribution, annual production, integrated subject areas, key source journals and keyword or term interactions). Although bibliometric studies on the present research theme are not frequent, our results are sub-optimal due to the small number of search query matches from the Scopus database. As a result, our findings offer only a fragmentary comprehension of the topics in question. Nevertheless, this review provides valuable inputs regarding prospective research avenues for researchers to pursue in the future.
  10. Fulltext Anti-HMG-CoA Reductase, Antioxidant, and Anti-Inflammatory Activities of Amaranthus viridis Leaf Extract as a Potential Treatment for Hypercholesterolemia
    Salvamani S, Gunasekaran B, Shukor MY, Shaharuddin NA, Sabullah MK, Ahmad SA
    Evid Based Complement Alternat Med, 2016;2016:8090841.
    PMID: 27051453 DOI: 10.1155/2016/8090841
    Inflammation and oxidative stress are believed to contribute to the pathology of several chronic diseases including hypercholesterolemia (elevated levels of cholesterol in blood) and atherosclerosis. HMG-CoA reductase inhibitors of plant origin are needed as synthetic drugs, such as statins, which are known to cause adverse effects on the liver and muscles. Amaranthus viridis (A. viridis) has been used from ancient times for its supposedly medically beneficial properties. In the current study, different parts of A. viridis (leaf, stem, and seed) were evaluated for potential anti-HMG-CoA reductase, antioxidant, and anti-inflammatory activities. The putative HMG-CoA reductase inhibitory activity of A. viridis extracts at different concentrations was determined spectrophotometrically by NADPH oxidation, using HMG-CoA as substrate. A. viridis leaf extract revealed the highest HMG-CoA reductase inhibitory effect at about 71%, with noncompetitive inhibition in Lineweaver-Burk plot analysis. The leaf extract showed good inhibition of hydroperoxides, 2,2-diphenyl-1-picrylhydrazyl (DPPH), nitric oxide (NO), and ferric ion radicals in various concentrations. A. viridis leaf extract was proven to be an effective inhibitor of hyaluronidase, lipoxygenase, and xanthine oxidase enzymes. The experimental data suggest that A. viridis leaf extract is a source of potent antioxidant and anti-inflammatory agent and may modulate cholesterol metabolism by inhibition of HMG-CoA reductase.
  11. Fulltext Coco Peat as Agricultural Waste Sorbent for Sustainable Diesel-Filter System
    Verasoundarapandian G, Zakaria NN, Shaharuddin NA, Khalil KA, Puasa NA, Azmi AA, et al.
    Plants (Basel), 2021 Nov 16;10(11).
    PMID: 34834831 DOI: 10.3390/plants10112468
    Oil spill incidents are hazardous and have prolonged damage to the marine environment. Management and spill clean-up procedures are practical and rapid, with several shortcomings. Coco peat (CP) and coco fibre (CF) are refined from coconut waste, and their abundance makes them desirable for diesel spillage treatment. Using a filter-based system, the selectivity of coco peat sorbent was tested using CP, CF and peat-fibre mix (CPM). CP exhibited maximal diesel sorption capacity with minimal seawater uptake, thus being selected for further optimisation analysis. The heat treatment considerably improved the sorption capacity and efficiency of diesel absorbed by CP, as supported by FTIR and VPSEM-EDX analysis. Conventional one-factor-at-a-time (OFAT) examined the performance of diesel sorption by CP under varying parameters, namely temperature, time of heating, packing density and diesel concentration. The significant factors were statistically evaluated using response surface methodology (RSM) via Plackett-Burman design (PB) and central composite design (CCD). Three significant (p < 0.05) factors (time, packing density and diesel concentration) were identified by PB and further analysed for interactions among the parameters. CCD predicted efficiency of diesel absorbed at 59.92% (71.90 mL) (initial diesel concentration of 30% v/v) and the experimental model validated the design with 59.17% (71.00 mL) diesel sorbed at the optimised conditions of 14.1 min of heating (200 °C) with packing density of 0.08 g/cm3 and 30% (v/v) of diesel concentration. The performance of CP in RSM (59.17%) was better than that in OFAT (58.33%). The discoveries imply that natural sorbent materials such as CP in oil spill clean-up operations can be advantageous and environmentally feasible. This study also demonstrated the diesel-filter system as a pilot study for the prospective up-scale application of oil spills.
  12. Functional characterization of the MSP-C6 promoter as a potential tool for mesocarp-preferential expression of transgenes
    Badai SS, Rasid OA, Masani MYA, Chan KL, Chan PL, Shaharuddin NA, et al.
    J Plant Physiol, 2023 Oct;289:154080.
    PMID: 37699261 DOI: 10.1016/j.jplph.2023.154080
    Modification of lipid composition in the mesocarp tissue of oil palm involves genetic manipulation of multiple genes. More than one mesocarp-preferential promoter is necessary for the expression of individual transgenes in the same plant to obviate transcriptional gene silencing. This study aimed to identify genes that are preferentially expressed in the mesocarp tissue and characterize selected candidate mesocarp-preferential promoters. Ten transcripts that were preferentially expressed in the mesocarp tissue were identified from the analysis of 82 transcriptome datasets of 12 different oil palm tissues. The expression of two candidate genes, MSP-C1 and MSP-C6, was verified to be preferentially expressed in the mesocarp tissues and shown to have a low expression level in non-mesocarp tissues by reverse transcription quantitative real-time PCR (RT-qPCR). MSP-C6 promoter fragments of different lengths were transformed into tomato plants for further characterization. Both unripe and ripe fruits of transgenic tomato plants transformed with a construct harboring the MSP-C6-F1 (2014 bp) promoter were shown to have high beta-glucuronidase (GUS) activities. The findings of this study suggest the potential applications of the MSP-C6 promoter as a molecular tool for genetic engineering of novel traits in fruit crops.
  13. Fulltext EgJUB1 and EgERF113 transcription factors as potential master regulators of defense response in Elaeis guineensis against the hemibiotrophic Ganoderma boninense
    Sakeh NM, Abdullah SNA, Bahari MNA, Azzeme AM, Shaharuddin NA, Idris AS
    BMC Plant Biol, 2021 Jan 22;21(1):59.
    PMID: 33482731 DOI: 10.1186/s12870-020-02812-7
    BACKGROUND: Hemibiotrophic pathogen such as the fungal pathogen Ganoderma boninense that is destructive to oil palm, manipulates host defense mechanism by strategically switching from biotrophic to necrotrophic phase. Our previous study revealed two distinguishable expression profiles of oil palm genes that formed the basis in deducing biotrophic phase at early interaction which switched to necrotrophic phase at a later stage of infection.

    RESULTS: The present report is a continuing study from our previous published transcriptomic profiling of oil palm seedlings against G. boninense. We focused on identifying differentially expressed genes (DEGs) encoding transcription factors (TFs) from the same RNA-seq data; resulting in 106 upregulated and 108 downregulated TFs being identified. The DEGs are involved in four established defense-related pathways responsible for cell wall modification, reactive oxygen species (ROS)-mediated signaling, programmed cell death (PCD) and plant innate immunity. We discovered upregulation of JUNGBRUNNEN 1 (EgJUB1) during the fungal biotrophic phase while Ethylene Responsive Factor 113 (EgERF113) demonstrated prominent upregulation when the palm switches to defense against necrotrophic phase. EgJUB1 was shown to have a binding activity to a 19 bp palindromic SNBE1 element, WNNYBTNNNNNNNAMGNHW found in the promoter region of co-expressing EgHSFC-2b. Further in silico analysis of promoter regions revealed co-expression of EgJUB1 with TFs containing SNBE1 element with single nucleotide change at either the 5th or 18th position. Meanwhile, EgERF113 binds to both GCC and DRE/CRT elements promoting plasticity in upregulating the downstream defense-related genes. Both TFs were proven to be nuclear-localized based on subcellular localization experiment using onion epidermal cells.

    CONCLUSION: Our findings demonstrated unprecedented transcriptional reprogramming of specific TFs potentially to enable regulation of a specific set of genes during different infection phases of this hemibiotrophic fungal pathogen. The results propose the intricacy of oil palm defense response in orchestrating EgJUB1 during biotrophic and EgERF113 during the subsequent transition to the necrotrophic phase. Binding of EgJUB1 to SNBE motif instead of NACBS while EgERF113 to GCC-box and DRE/CRT motifs is unconventional and not normally associated with pathogen infection. Identification of these phase-specific oil palm TFs is important in designing strategies to tackle or attenuate the progress of infection.

  14. Fulltext Proteome of rice roots treated with exogenous proline
    Teh CY, Ho CL, Shaharuddin NA, Lai KS, Mahmood M
    3 Biotech, 2019 Mar;9(3):101.
    PMID: 30800612 DOI: 10.1007/s13205-019-1615-x
    Proteomic analysis was conducted to identify the rice root proteins induced by exogenous proline and their involvement in root growth. Proteins were extracted from the root tissues grown under two conditions, T1 (control) and T2 (10 mM proline), and profiled by two-dimensional polyacrylamide gel electrophoresis. Seventeen of 30 differentially expressed proteins were identified by mass spectrometry. Proline-treated rice roots showed up-regulation and down-regulation of nine and eight proteins, respectively, when compared to those in the control. Among the differentially expressed proteins, the down-regulation of glutathione reductase and peroxidase could be involved in the regulation of cellular hydrogen peroxide and reactive oxygen species levels that modulate the root cell wall structure. Differentially expressed proteins identified as pathogenesis-related proteins might be related to stress adaptive mechanisms in response to exogenous proline treatment. In addition, differentially expressed protein identified as the fructose-bisphosphate aldolases and cytochrome c oxidase might be associated with energy metabolism, which is needed during root developmental process. This is the first attempt to study the changes in rice root proteome treated with proline. The acquired information could open new avenues for further functional studies on the involvement of proline in modulating root development and its relation to stress adaptation of plants.
  15. Towards a better understanding of Artemisia vulgaris: Botany, phytochemistry, pharmacological and biotechnological potential
    Abiri R, Silva ALM, de Mesquita LSS, de Mesquita JWC, Atabaki N, de Almeida EB, et al.
    Food Res Int, 2018 07;109:403-415.
    PMID: 29803465 DOI: 10.1016/j.foodres.2018.03.072
    Artemisia vulgaris is one of the important medicinal plant species of the genus Artemisia, which is usually known for its volatile oils. The genus Artemisia has become the subject of great interest due to its chemical and biological diversity as well as the discovery and isolation of promising anti-malarial drug artemisinin. A. vulgaris has a long history in treatment of human ailments by medicinal plants in various parts of the world. This medicinal plant possesses a broad spectrum of therapeutic properties including: anti-malarial, anti-inflammatory, anti-hypertensive, anti-oxidant, anti-tumoral, immunomodulatory, hepatoprotective, anti-spasmodic and anti-septic. These activities are mainly attributed to the presence of various classes of secondary metabolites, including flavonoids, sesquiterpene lactones, coumarins, acetylenes, phenolic acids, organic acids, mono- and sesquiterpenes. Studies related to A. vulgaris morphology, anatomy and phytochemistry has gained a significant interest for better understanding of production and accumulation of therapeutic compounds in this species. Recently, phytochemical and pharmacological investigations have corroborated the therapeutic potential of bioactive compounds of A. vulgaris. These findings provided further evidence for gaining deeper insight into the identification and isolation of novel compounds, which act as alternative sources of anti-malarial drugs in a cost-effective manner. Considering the rising demand and various medical applications of A. vulgaris, this review highlights the recent reports on the chemistry, biological activities and biotechnological interventions for controlled and continuous production of bioactive compounds from this plant species.
  16. Fulltext Structure and Principal Components Analyses Reveal an Intervarietal Fusion in Malaysian Mistletoe Fig (Ficus deltoidea Jack) Populations
    Zimisuhara B, Valdiani A, Shaharuddin NA, Qamaruzzaman F, Maziah M
    Int J Mol Sci, 2015 Jun 24;16(7):14369-94.
    PMID: 26114389 DOI: 10.3390/ijms160714369
    Genetic structure and biodiversity of the medicinal plant Ficus deltoidea have rarely been scrutinized. To fill these lacunae, five varieties, consisting of 30 F. deltoidea accessions were collected across the country and studied on the basis of molecular and morphological data. Molecular analysis of the accessions was performed using nine Inter Simple Sequence Repeat (ISSR) markers, seven of which were detected as polymorphic markers. ISSR-based clustering generated four clusters supporting the geographical distribution of the accessions to some extent. The Jaccard's similarity coefficient implied the existence of low diversity (0.50-0.75) in the studied population. STRUCTURE analysis showed a low differentiation among the sampling sites, while a moderate varietal differentiation was unveiled with two main populations of F. deltoidea. Our observations confirmed the occurrence of gene flow among the accessions; however, the highest degree of this genetic interference was related to the three accessions of FDDJ10, FDTT16 and FDKT25. These three accessions may be the genetic intervarietal fusion points of the plant's population. Principal Components Analysis (PCA) relying on quantitative morphological characteristics resulted in two principal components with Eigenvalue >1 which made up 89.96% of the total variation. The cluster analysis performed by the eight quantitative characteristics led to grouping the accessions into four clusters with a Euclidean distance ranged between 0.06 and 1.10. Similarly, a four-cluster dendrogram was generated using qualitative traits. The qualitative characteristics were found to be more discriminating in the cluster and PCA analyses, while ISSRs were more informative on the evolution and genetic structure of the population.
  17. GCTTCA as a novel motif for regulating mesocarp-specific expression of the oil palm (Elaeis guineensis Jacq.) stearoyl-ACP desaturase gene
    Hanifiah FHA, Abdullah SNA, Othman A, Shaharuddin NA, Saud HM, Hasnulhadi HAH, et al.
    Plant Cell Rep, 2018 Aug;37(8):1127-1143.
    PMID: 29789886 DOI: 10.1007/s00299-018-2300-y
    KEY MESSAGE: TAAAAT and a novel motif, GCTTCA found in the oil palm stearoyl-ACP desaturase (SAD1) promoter are involved in regulating mesocarp-specific expression. Two key fatty acid biosynthetic genes, stearoyl-ACP desaturase (SAD1), and acyl-carrier protein (ACP3) in Elaeis guineensis (oil palm) showed high level of expression during the period of oil synthesis in the mesocarp [12-19 weeks after anthesis (w.a.a.)] and kernel (12-15 w.a.a.). Both genes are expressed in spear leaves at much lower levels and the expression increased by 1.5-fold to 2.5-fold following treatments with ethylene and abscisic acid (ABA). Both SAD1 and ACP3 promoters contain phytohormone-responsive, light-responsive, abiotic factors/wounding-responsive, endosperm specificity and fruit maturation/ripening regulatory motifs. The activities of the full length and six 5' deletion fragments of the SAD1 promoter were analyzed in transiently transformed oil palm tissues by quantitative β-glucuronidase (GUS) fluorometric assay. The highest SAD1 promoter activity was observed in the mesocarp followed by kernel and the least in the leaves. GUS activity in the D3 deletion construct (- 486 to + 108) was the highest, while the D2 (- 535 to + 108) gave the lowest suggesting the presence of negative cis-acting regulatory element(s) in the deleted - 535 to - 486 (49 bp). It was found that the 49-bp region binds to the nuclear protein extract from mesocarp but not from leaves in electrophoretic mobility shift assay (EMSA). Further fine-tuned analysis of this 49-bp region using truncated DNA led to the identification of GCTTCA as a novel motif in the SAD1 promoter. Interestingly, another known fruit ripening-related motif, LECPLEACS2 (TAAAAT) was found to be required for effective binding of the novel motif to the mesocarp nuclear protein extract.
  18. Fulltext Molecular cloning and characterization of novel phytocystatin gene from turmeric, Curcuma longa
    Chan SN, Abu Bakar N, Mahmood M, Ho CL, Shaharuddin NA
    Biomed Res Int, 2014;2014:973790.
    PMID: 25853138 DOI: 10.1155/2014/973790
    Phytocystatin, a type of protease inhibitor (PI), plays major roles in plant defense mechanisms and has been reported to show antipathogenic properties and plant stress tolerance. Recombinant plant PIs are gaining popularity as potential candidates in engineering of crop protection and in synthesizing medicine. It is therefore crucial to identify PI from novel sources like Curcuma longa as it is more effective in combating against pathogens due to its novelty. In this study, a novel cDNA fragment encoding phytocystatin was isolated using degenerate PCR primers, designed from consensus regions of phytocystatin from other plant species. A full-length cDNA of the phytocystatin gene, designated CypCl, was acquired using 5'/3' rapid amplification of cDNA ends method and it has been deposited in NCBI database (accession number KF545954.1). It has a 687 bp long open reading frame (ORF) which encodes 228 amino acids. BLAST result indicated that CypCl is similar to cystatin protease inhibitor from Cucumis sativus with 74% max identity. Sequence analysis showed that CypCl contains most of the motifs found in a cystatin, including a G residue, LARFAV-, QxVxG sequence, PW dipeptide, and SNSL sequence at C-terminal extension. Phylogenetic studies also showed that CypCl is related to phytocystatin from Elaeis guineensis.
  19. Fulltext RNA-Seq analysis revealed genes associated with UV-induced cell necrosis through MAPK/TNF-α pathways in human dermal fibroblast cells as an inducer of premature photoaging
    Alafiatayo AA, Lai KS, Ahmad S, Mahmood M, Shaharuddin NA
    Genomics, 2020 01;112(1):484-493.
    PMID: 30946891 DOI: 10.1016/j.ygeno.2019.03.011
    Exposing the skin to solar UV radiation induces cascades of signaling pathways and biological alterations such as redox imbalance, suppression of antioxidant genes and programmed cell death. Therefore, the aim of this study was to use RNA-Seq to unravel the effects of UV radiation on Normal Human Adult Fibroblast cells (NHDF). Cells were exposed to UV (20 mJ/cm2 for 3 mins) and incubated for 24 h. Total mRNA from the cells generated libraries of 72,080,648 and 40,750,939 raw reads from UV-treated and control cells respectively. Of the differentially expressed genes (DEGs) produced 2,007 were up-regulated and 2,791 were down-regulated (fold change ≥2, p 
  20. Fulltext Identification of Oil Palm's Consistently Upregulated Genes during Early Infections of Ganoderma boninense via RNA-Seq Technology and Real-Time Quantitative PCR
    Zuhar LM, Madihah AZ, Ahmad SA, Zainal Z, Idris AS, Shaharuddin NA
    Plants (Basel), 2021 Sep 27;10(10).
    PMID: 34685835 DOI: 10.3390/plants10102026
    Basal stem rot (BSR) disease caused by pathogenic fungus Ganoderma boninense is a significant concern in the oil palm industry. G. boninense infection in oil palm induces defense-related genes. To understand oil palm defense mechanisms in response to fungal invasion, we analyzed differentially expressed genes (DEGs) derived from RNA-sequencing (RNA-seq) transcriptomic libraries of oil palm roots infected with G. boninense. A total of 126 DEGs were detected from the transcriptomic libraries of G. boninense-infected root tissues at different infection stages. Functional annotation via pathway enrichment analyses revealed that the DEGs were involved in the defense response against the pathogen. The expression of the selected DEGs was further confirmed using real-time quantitative PCR (qPCR) on independent oil palm seedlings and mature palm samples. Seven putative defense-related DEGs consistently showed upregulation in seedlings and mature plants during G. boninense infection. These seven genes might potentially be developed as biomarkers for the early detection of BSR in oil palm.
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